Small molecule regulators of mitochondrial fusion and methods of use thereof

ABSTRACT

Compositions comprising small molecule mitofusin agonists are described. The mitofusin modulating agents are useful for treating diseases or disorders associated with a mitochondria-associated disease, disorder, or condition such as diseases or disorders associated with mitofusin 1 (Mfn1) and/or mitofusin 2 (Mfn2), or mitochondrial dysfunction. Methods of treatment, pharmaceutical formulations, and screening methods for identifying compounds that regulate mitochondrial function are also described.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of PCT application numberPCT/US2018/028514 filed on Apr. 20, 2018, which claims priority fromU.S. Provisional Application Ser. No. 62/488,787 filed on 23 Apr. 2017and U.S. Provisional Application Ser. No. 62/584,515 filed on 10 Nov.2017, each of which are incorporated herein by reference in theirentireties.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant number HL135736 awarded by National Institutes of Health. The government hascertain rights in the invention.

MATERIAL INCORPORATED-BY-REFERENCE

The Sequence Listing, which is a part of the present disclosure,includes a computer readable form comprising nucleotide and/or aminoacid sequences of the present invention. The subject matter of theSequence Listing is incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present disclosure generally relates to compositions and methods fortreating mitochondria-associated diseases, disorders, or conditions.Also provided are methods for screening compositions.

SUMMARY OF THE INVENTION

Among the various aspects of the present disclosure is the provision ofa small molecule regulator of mitochondrial fusion and methods of usethereof.

One aspect of the present disclosure provides for a method of treating amitochondria-associated disease, disorder, or condition. In someembodiments, the method comprises administering to a subject atherapeutically effective amount of a composition comprising one or moreof a mitofusin modulating agent or a pharmaceutically acceptable saltthereof, wherein the mitofusin modulating agent is a mitofusin agonist;the mitofusin modulating agent regulates mitochondrial fusion; or themitofusin modulating agent is not a compound of TABLE 4.

Another aspect of the present disclosure provides for a method ofmodulating mitofusin in a subject in need thereof. In some embodiments,the method comprises administering to a subject a composition comprisinga mitofusin modulating agent or a pharmaceutically acceptable saltthereof; wherein, the mitofusin modulating agent is a mitofusin agonist;the mitofusin modulating agent regulates mitochondrial fusion; thesubject has a mitochondria-associated disease, disorder, or condition;or the mitofusin modulating agent is not a compound of TABLE 4.

Another aspect of the present disclosure provides for a method ofenhancing mitochondrial trafficking in nerve axons in a subject in needthereof. In some embodiments, the method comprises administering to asubject a composition comprising a mitofusin modulating agent or apharmaceutically acceptable salt thereof; wherein, the mitofusinmodulating agent is a mitofusin agonist; the mitofusin modulating agentregulates mitochondrial fusion; the subject has amitochondria-associated disease, disorder, or condition; or themitofusin modulating agent is not a compound of TABLE 4.

In some embodiments, the mitochondria-associated disease, disorder, orcondition is selected from one or more of the group consisting of: achronic neurodegenerative condition wherein mitochondrial fusion,fitness, or trafficking are impaired; a disease or disorder associatedwith mitofusin 1 (Mfn1) or mitofusin 2 (Mfn2) or mitochondrialdysfunction, fragmentation, or fusion; dysfunction in Mfn1 or Mfn2unfolding; mitochondria dysfunction caused by mutations; a degenerativeneurological condition, such as Alzheimer's, Parkinson's, Charcot MarieTooth Disease, or Huntington's diseases; or hereditary motor and sensoryneuropathy, autism, autosomal dominant optic atrophy (ADOA), musculardystrophy, Lou Gehrig's disease, cancer, mitochondrial myopathy,Diabetes mellitus and deafness (DAD), Leber's hereditary opticneuropathy (LHON), Leigh syndrome, subacute sclerosing encephalopathy,Neuropathy, ataxia, retinitis pigmentosa, and ptosis (NARP),Myoneurogenic gastrointestinal encephalopathy (MNGIE), MyoclonicEpilepsy with Ragged Red Fibers (MERRF), Mitochondrial myopathy,encephalomyopathy, lactic acidosis, stroke-like symptoms (MELAS), mtDNAdepletion, mitochondrial neurogastrointestinal encephalomyopathy(MNGIE), Dysautonomic Mitochondrial Myopathy, MitochondrialChannelopathy, or pyruvate dehydrogenase complex deficiency (PDCD/PDH).

In some embodiments, the neurodegenerative condition is selected fromCharcot Marie Tooth disease, Huntington's disease, Parkinson's disease,Alzheimer's disease, or amyotrophic lateral sclerosis (ALS).

In some embodiments, the mitofusin modulating agent is a small moleculemimetic of a Mfn2 peptide-peptide interface.

In some embodiments, the mitofusin modulating agent: has substantiallysimilar functional potency and specificity of both1-[2-(benzylsulfanyl)ethyl]-3-(2-methylcyclohexyl)urea (Cpd A) and2-{2-[(5-cyclopropyl-4-phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]propanamido}-4H,5H,6H-cyclopenta[b]thiophene-3-carboxamide(Cpd B); targets at least two phosphorylated forms of MFN; or stimulatesmitofusin activity (e.g., fusion and trafficking).

In some embodiments, the mitofusin modulating agent: enhancesmitochondrial trafficking in nerve axons; increases microsomalstability; corrects cell and organ dysfunction caused by primaryabnormalities in mitochondrial fission or fusion; reverses mitochondrialdefects (e.g., dysmorphometry); restores, activates, regulates,modulates, promotes, or enhances the fusion, function, tethering,transport, trafficking (e.g., axonal mitochondrial trafficking),mobility, or movement of mitochondria (in, optionally, a nerve or aneuron); enhances mitochondrial elongation or mitochondrial elongationaspect ratio; disrupts intramolecular restraints in Mfn2; allostericallyactivates Mfn2; corrects mitochondrial dysfunction and cellulardysfunction; repairs defects in neurons with mitochondrial mutations; ortargets Mfn1 or Mfn2.

In some embodiments, the mitofusin modulating agent is selected from acompound of formula:

or a pharmaceutically acceptable salt, tautomer, or stereoisomer thereofwherein, R¹ is selected from the group consisting of C₁₋₈ alkyl, C₁₋₈alkyl substituted with S, S, thiophene, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, thiophene, and thiophene carboxamide; R²is selected from the group consisting of C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, imidazole, thiophene, thiophenecarboxamide, and triazole; R³ is selected from the group consisting ofhydrogen (H) and C₁₋₈ alkyl; R⁴ is selected form the group consisting ofhydrogen (H) and C₁₋₈ alkyl; R⁵ is selected from the group consisting ofC₁₋₈ alkyl, C₁₋₈ alkyl substituted with S, S, thiophene, C₃₋₈cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, thiophene, thiophenecarboxamide, and triazole; R⁶ is selected from the group consisting ofbicyclononanone, pyrrole, benzimidizole, pyrrole substituted pyrrole,and substituted benzimidizole; R⁷ is selected from the group consistingof C₁₋₈ alkyl, pyrrole, pyrrole substituted pyrrole, benzimidizole, andsubstituted benzimidizole; R⁸ is selected from the group consisting ofhydrogen (H); R⁹ is selected from the group consisting of C₁₋₈ alkyl,pyrrole, substituted pyrrole, pyrrole substituted pyrrole,benzimidizole, and substituted benzimidizole; A is selected from thegroup consisting of a bond, S, C, O, and N; X is selected from the groupconsisting of O, C, and N;

Y is selected from the group consisting of O, C, and N; and Z is alinker group selected from the group consisting of a bond or C₁₋₆ alkyl;and optionally, R¹ and R² form a cyclic group, R¹ and R⁴ form a cyclicgroup, R² and R³ form a cyclic group, R⁴ and R³ form a cyclic group; orR⁸ and R⁷ form a cyclic group, wherein, the bicyclononanone optionallycomprises one or more N atoms.

In some embodiments, the mitofusin modulating agent is selected from acompound of

wherein, R¹ is selected from the group consisting of

R² is selected from the group consisting of

R³ is selected from the group consisting of hydrogen (H) and C₁₋₈ alkyl;R⁴ is selected form the group consisting of hydrogen (H) and C₁₋₈ alkyl;A is a bond, S, SO, SO₂, C, or O;

X is N; Y is N; and Z is a linker group selected from the groupconsisting of a bond or C₁₋₆ alkyl.

In some embodiments, R¹, R², R³, or R⁴ are optionally substituted by oneor more of: acetamide, C₁₋₈ alkoxy, amino, azo, Br, C₁₋₈ alkyl,carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O, phenyl, S,sulfoxide, sulfur dioxide, or thiophene; and optionally furthersubstituted with one or more acetamide, alkoxy, amino, azo, Br, C₁₋₈alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl,C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O, phenyl, S,sulfoxide, sulfur dioxide, or thiophene; wherein, the alkyl, cycloalkyl,heteroaryl, heterocyclyl, indole, or phenyl, is optionally furthersubstituted with one or more selected from the group consisting ofacetamide, alkoxy, amino, azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl,cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F,halo, indole, N, nitrile, O, phenyl, S, sulfoxide, sulfur dioxide, orthiophene.

In some embodiments, the compound is selected from the group consistingof:

In some embodiments, the compound is selected from the group consistingof:

Yet another aspect of the present disclosure provides for a compound offormula:

or a pharmaceutically acceptable salt, tautomer, or stereoisomer thereofwherein, R¹ is selected from the group consisting of C₁₋₈ alkyl, C₁₋₈alkyl substituted with S, S, thiophene, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, thiophene, and thiophene carboxamide; R²is selected from the group consisting of C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, imidazole, thiophene, thiophenecarboxamide, and triazole; R³ is selected from the group consisting ofhydrogen (H) and C₁₋₈ alkyl; R⁴ is selected form the group consisting ofhydrogen (H) and C₁₋₈ alkyl; R⁵ is selected from the group consisting ofC₁₋₈ alkyl, C₁₋₈ alkyl substituted with S, S, thiophene, C₃₋₈cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, thiophene, thiophenecarboxamide, and triazole; R⁶ is selected from the group consisting ofbicyclononanone, pyrrole, benzimidizole, pyrrole substituted pyrrole,and substituted benzimidizole; R⁷ is selected from the group consistingof C₁₋₈ alkyl, pyrrole, pyrrole substituted pyrrole, benzimidizole, andsubstituted benzimidizole; R⁸ is selected from the group consisting ofhydrogen (H); R⁹ is selected from the group consisting of C₁₋₈ alkyl,pyrrole, substituted pyrrole, pyrrole substituted pyrrole,benzimidizole, and substituted benzimidizole; X is selected from thegroup consisting of O, C, and N; Y is selected from the group consistingof O, C, and N; or Z is a linker group selected from the groupconsisting of a bond or C₁₋₆ alkyl.

In some embodiments, R¹ and R² form a cyclic group, R¹ and R⁴ form acyclic group, R² and R³ form a cyclic group, R⁴ and R³ form a cyclicgroup; or R⁸ and R⁷ form a cyclic group, wherein, the bicyclononanoneoptionally comprises one or more N atoms; or formula (I), (II), or (III)is not a compound of TABLE 4, TABLE 5, TABLE 7, or

In some embodiments, R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, or R⁹ areoptionally substituted by one or more of: acetamide, C₁₋₈ alkoxy, amino,azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl,C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N,nitrile, O, phenyl, S, sulfoxide, sulfur dioxide, or thiophene; oroptionally further substituted with one or more acetamide, alkoxy,amino, azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo,indole, N, nitrile, O, phenyl, S, sulfoxide, sulfur dioxide, orthiophene; wherein, the alkyl, cycloalkyl, heteroaryl, heterocyclyl,indole, or phenyl, is optionally further substituted with one or moreselected from the group consisting of acetamide, alkoxy, amino, azo, Br,C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O,phenyl, S, sulfoxide, sulfur dioxide, or thiophene.

In some embodiments, the compound is of formula

wherein,

R¹ is selected from the group consisting of

R² is selected from the group consisting of

R³ is selected from the group consisting of hydrogen (H) and C₁₋₈ alkyl;R⁴ is selected form the group consisting of hydrogen (H) and C₁₋₈ alkyl;A is a bond, S, SO, SO₂, C, or O;

X is N; Y is N; or Z is a linker group selected from the groupconsisting of a bond or C₁₋₆ alkyl.

In some embodiments, R¹, R², R³, or R⁴ are optionally substituted by oneor more of: acetamide, C₁₋₈ alkoxy, amino, azo, Br, C₁₋₈ alkyl,carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O, phenyl, S,sulfoxide, sulfur dioxide, or thiophene; and optionally furthersubstituted with one or more acetamide, alkoxy, amino, azo, Br, C₁₋₈alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl,C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O, phenyl, S,sulfoxide, sulfur dioxide, or thiophene; wherein, the alkyl, cycloalkyl,heteroaryl, heterocyclyl, indole, or phenyl, is optionally furthersubstituted with one or more selected from the group consisting ofacetamide, alkoxy, amino, azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl,cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F,halo, indole, N, nitrile, O, phenyl, S, sulfoxide, sulfur dioxide, orthiophene.

In some embodiments, the compound is selected from:

In some embodiments, the compound is selected from:

In some embodiments, the compound is a small molecule mimetic of a Mfn2peptide-peptide interface.

In some embodiments, the compound targets at least two phosphorylatedforms of MFN; enhances mitochondrial trafficking in nerve axons;increases microsomal stability; corrects cell and organ dysfunctioncaused by primary abnormalities in mitochondrial fission or fusion;reverses mitochondrial defects (e.g., dysmorphometry); restores,activates, regulates, modulates, promotes, or enhances the fusion,function, tethering, transport, trafficking (e.g., axonal mitochondrialtrafficking), mobility, or movement of mitochondria (in, optionally, anerve or a neuron); enhances mitochondrial elongation or mitochondrialelongation aspect ratio; disrupts intramolecular restraints in Mfn2;allosterically activates Mfn2; corrects mitochondrial dysfunction andcellular dysfunction; repairs defects in neurons with mitochondrialmutations; or targets Mfn1 or Mfn2.

Yet another aspect of the present disclosure provides for apharmaceutical composition comprising a compound of formula (I), (II),or (Ill), optionally in combination with one or more therapeuticallyacceptable diluents or carriers.

In some embodiments, the pharmaceutical composition comprises apharmaceutically acceptable excipient.

In some embodiments, the pharmaceutical composition comprises a at leastone compound selected from the group consisting of neuroprotectants,antiparkinsonian drugs, amyloid protein deposition inhibitors, betaamyloid synthesis inhibitors, antidepressants, anxiolytic drugs,antipsychotic drugs, anti-amyotrophic lateral sclerosis drugs,anti-Huntington's drugs, anti-Alzheimer's drugs, anti-epileptic drugs,or steroids.

Yet another aspect of the present disclosure provides for a method oftreating a mitochondria-associated disease, disorder, or condition in asubject comprising administering to the subject a therapeuticallyeffective amount of a mitofusin modulating agent comprising the compoundof formula (I), (II), or (Ill).

In some embodiments, the subject is diagnosed with or is suspected ofhaving a mitochondria-associated disease.

In some embodiments, the mitochondria-associate disease is selected fromone or more of the group consisting of: a chronic neurodegenerativecondition wherein mitochondrial fusion, fitness, or trafficking areimpaired; a disease or disorder associated with mitofusin 1 (Mfn1) ormitofusin 2 (Mfn2) or mitochondrial dysfunction, fragmentation, orfusion; dysfunction in Mfn1 or Mfn2 unfolding; mitochondria dysfunctioncaused by mutations; a degenerative neurological condition, such asAlzheimer's, Parkinson's, Charcot Marie Tooth Disease, or Huntington'sdiseases; diabetes-induced neuropathy, or heart disease; or hereditarymotor and sensory neuropathy, autism, autosomal dominant optic atrophy(ADOA), muscular dystrophy, Lou Gehrig's disease, cancer, mitochondrialmyopathy, Diabetes mellitus and deafness (DAD), Leber's hereditary opticneuropathy (LHON), Leigh syndrome, subacute sclerosing encephalopathy,Neuropathy, ataxia, retinitis pigmentosa, and ptosis (NARP),Myoneurogenic gastrointestinal encephalopathy (MNGIE), MyoclonicEpilepsy with Ragged Red Fibers (MERRF), Mitochondrial myopathy,encephalomyopathy, lactic acidosis, stroke-like symptoms (MELAS), mtDNAdepletion, mitochondrial neurogastrointestinal encephalomyopathy(MNGIE), Dysautonomic Mitochondrial Myopathy, MitochondrialChannelopathy, or pyruvate dehydrogenase complex deficiency (PDCD/PDH).

Other objects and features will be in part apparent and in part pointedout hereinafter.

DESCRIPTION OF THE DRAWINGS

Those of skill in the art will understand that the drawings, describedbelow, are for illustrative purposes only. The drawings are not intendedto limit the scope of the present teachings in any way.

FIG. 1 is a series of hypothetical structures of human MFN2 modeledusing I-TASSER. (top) MFN2 modeled in a closed configuration based onstructural homology with Homo sapiens MFN1 and Arabidopsis thalianadynamin-related protein. (bottom) MFN2 modeled in an open configurationbased on structural homology with Homo sapiens Opal. Exploded views showcritical HR1 (green)-HR2 (red) interactions in orthogonal views.

FIG. 2A, FIG. 2B, FIG. 2C, FIG. 2D, FIG. 2E, FIG. 2F, FIG. 2G and FIG.2H are a series of images and graphs showing MFN2 Ser³⁷⁸ phosphorylationby PINK1 regulates mitochondrial fusion. (A) Amino acid sequencesurrounding fusion-promoting MFN2 peptide. Side chain characteristics(H, hydrophobic; +, basic; −, acidic) are above. (B) Mitochondrialfusion stimulated by N- and C-terminal minipeptides. Aspect ratio ismitochondrial long axis/short axis. Inset: Fusion in MFN1- and MFN2-nullMEFs. (C) Alanine (A) scanning of minipeptide 374-384 fusion activity.(D) Ser378 substitution analysis of minipeptide 374-384 fusion activity.p values in D and E are vs parent minipeptide 374-384 (ANOVA). (E)Binding of minipeptides with Ser378 substitutions to HR2 target sequence(n=6). (F) Binding of Asp378 minipeptide to HR2 target sequence before(left) and after (right) Ala substitution for putative interacting aminoacids. (G) Ion chromatograms from assigned MFN2 Ser378 phosphopeptidefragment ions after incubation with PINK1 kinase (top) and stableisotope-labeled synthetic counterpart (bottom); proportional intensitiesare in adjacent stack plots. (H) Mitochondrial fusion promoted by MFN2Ser378 mutants with and without PINK1 kinase; immunoblot of proteinexpression at bottom. p values are by ANOVA.

FIG. 3 shows the purification of mitofusin agonist compounds A and B. Atthe top are high performance liquid chromatography and mass spectra ofcompounds as they were obtained from the commercial vendor. On thebottom are spectra after in-house purification. Cpd A: expected m/z306.18, exact mass found 307.3 [M+H]⁺; Cpd B: expected m/z 453.15, exactmass found 454.3 [M+H]⁺.

FIG. 4A and FIG. 4B are a series of chemical structures and a bar graphthat shows the structure and function of compounds A and B, morespecifically, the mitofusin-dependent mitochondrial elongation provokedby prototype Mfn agonist peptide mimetics (compounds A and B). FIG. 4Ashows 3D structures of1-[2-(benzylsulfanyl)ethyl]-3-(2-methylcyclohexyl)urea, designatedcompound A, and2-{2-[(5-cyclopropyl-4-phenyl-4H-1,2,4-triazol-3yl)sulfanyl]propanamido}-4H,5H,6H-cyclopenta[b]thiophene-3-carboxamide, designatedcompound B. FIG. 4B shows that mitochondrial elongation (increasedmitochondrial aspect ratio) evoked by compounds A and B requires eitherMfn1 or Mfn2 and each of compound A and compound B inhibited Mfn1 orMfn2. Note that there was no effect on mitochondrial elongation whenboth Mfn1 and Mfn2 were absent (see e.g., Example 2). Black bars arecompound-treated cells and white bars are vehicle (DMSO) treated.*=P<0.05 vs control (white).

FIG. 5A, FIG. 5B, FIG. 5C, and FIG. 5D are a series of bar graphs,structures, graphs, and images showing that small molecule HR1 MP374-384mimetics can be mitofusin agonists. (A) Functional screening for class Aand B small mitofusin agonists. 1 μM of each candidate compound wasadded to MFN2-deficient MEFs overnight. Mitochondrial aspect ratio is onleft and cell viability on right. Structures of the class A and Bchemosimilars are shown below (n=3; p values are by ANOVA with Tukey'spost hoc comparison). Black bars indicate class A and B compoundsselected for detailed studies. (B) Representative confocal images fromstudies in (A). Mitochondria were visualized with MitoTracker Orange.Cell viability was assessed simultaneously with mitochondrial aspectratio—live cells have green cytoplasm (calcein AM) and dead cells lackcalcein staining and have purple nuclei (red ethidium homodimeroverlying blue Hoechst). Scale bars are 10 μm. (C) Initial dose-responserelations of five fusogenic compounds from screening in (A). EC₅₀ values(indexed to the 100% maximal response elicited by the most effectivecompound, B1) are shown for the agonists with strong fusion-promotingactivity; mean±SEM of 3 independent studies for each compound. (D)Competition of the HR1 minipeptide at its MFN2 HR2 binding site by fivefusogenic compounds from (A). IC₅₀ values are shown for agonistswith >50% displacement (mean±SEM of 6 independent experiments percompound). Displacement curves for compounds A and B are re-plotted inFIG. 11C.

FIG. 6A, FIG. 6B, FIG. 6C and FIG. 6D are a series of line and bargraphs, images, and structures showing compounds A and B synergisticallypromote mitochondrial fusion by acting upon different mitofusinconformational states and displaying the EC50 values of compounds A andB and a key phosphorylation site in Mfn2. FIG. 6A shows A+B synergism.More specifically, that the EC50 values of compounds A and B were each100-200 nM. Note that when added in equal amounts, compounds A and Bsynergistically promoted mitochondrial elongation, with a combined EC50of ˜40 nM and a ˜25% greater maximal increase in mitochondrial aspectratio. FIG. 6B is a bar graph showing a negative charge conferred bySer378 phosphorylation or Asp (D) substitution is essential formini-peptide fusion promoting activity and shows how a S378D mutation,which mimics phosphorylation of this site, influenced Mfn2 conformationand function similarly to HR1 peptide 374-384 (see e.g., Example 2).FIG. 6C is a series of images showing representative confocalmicrographs of cells treated with mini-peptides in compound B. FIG. 6Dis a series of images showing the structural consequences of Ser378phosphorylation on the Mfn2 HR1-HR2 interacting face; His 380 rotatesout and Leu379 rotates in.

FIG. 7A, FIG. 7B and FIG. 7C are a series of structures and graphsshowing the evaluation of chimeric small molecule mitofusin agonists.(A) Structures of compounds A and B and their chimeras. (B)Dose-response of compounds in (A) to promote mitochondrial fusion(increase in aspect ratio) in MFN2-deficient MEFs. Data for compounds Aand B and chimera B-A/I in FIG. 11B are re-plotted here for comparison.(C) Comparison of EC50 values calculated from studies in panel B. pvalues are from ANOVA with Tukey's test.

FIG. 8 is a series of immunofluorescence images from cultured mouseneurons. Neurons with the human Charcot Marie Tooth disease mutation,Mfn2 T105M, exhibited increased mitochondrial fragmentation and neuronalpathology compared to control. Note how administration of compoundsrepaired the defects in mutant neurons (see e.g., Example 2).

FIG. 9A, FIG. 9B, FIG. 9C, FIG. 9D, and FIG. 9E are a series of bargraphs and images showing mitofusin agonists correct mitochondrialdamage induced by nonfunctioning MFN2 mutants by activating endogenousmitofusins. (A) Effects of mitofusin agonists in mitofusin-deficientcells expressing WT or mutant MFN2 (n=3 each). (B) Same as (A) inMFN1^(+/+,) MFN2^(−/−) cells. (C) Representative mitochondrial pathologyin cultured neonatal mouse neurons expressing MFN2 R94Q and correctionby mitofusin agonists. Immunoblot showing MFN2R94Q expression inindividual mouse pups is above. Scale bars are 21 mm; expanded views arefrom white squares. (D) Group data for studies in (C). (E) Results ofsimilar studies in cultured neonatal mouse neurons expressing MFN2T105M.

FIG. 10 is illustration showing Mfn agonist peptide binding and itsdisplacement by compounds A and B. The schematic demonstrates componentsof the system, depicting FITC labeled peptide binding to its immobilizedtarget (top) and displacement of the FITC peptide by competing smallmolecule.

FIG. 11A, FIG. 11B, FIG. 11C, FIG. 11D, FIG. 11E, FIG. 11F, and FIG. 11Garea series of images and graphs showing small molecule mimetics of MFN2HR1 amino acid side chains that interact with HR2 are mitofusinagonists. (A) (top) Three dimensional representations of minipeptideconformations driven by Ser378 phosphorylation, and (bottom) theirrespective small molecule mimetics. (B) Dose-dependent mitofusin agonismby small molecule agonists (n=6 each). (C) Displacement of minipeptide374-384 from its HR2 binding site by mitofusin agonists (n=3 each). (D)Restoration of MFN2 T105M-impaired mitochondrial fusion in MEFs bymitofusin agonists. (E) Selectivity of a class A, but not a class B,mitofusin agonist for Ser³⁷⁸-phosphorylated MFN2. (F) Impaired basalfunction, but normal proportional agonist responsiveness, of MFN2mutations altering HR1-HR2 interacting amino acids. (G) Change in FRETevoked by mitofusin agonists as a function of Ser378 mutant; decreasedFRET reflects conformational opening.

FIG. 12A, FIG. 12B and FIG. 12C are a series of drawings that diagramthe working model of Mfn2 conformation and function and Mfnfolding/unfolding measured by FRET. FIG. 8 shows that HR1 and HR2 domaininteraction can result in a folded conformation in which tethering toadjacent Mfn proteins is unfavorable. Disruption of HR1 and HR2 domainscan result in an unfolded conformation in which tethering is favorable.FIG. 12A-FIG. 12B are illustrations of change in FRET signaling evokedby Mfn conformation. FIG. 12C is a graph of a representative experimentwith changes in Δ80-275 Mfn2 FRET signal provoked by Mfn antagonist MP2and agonist MP1. This novel Forster resonance energy transfer (FRET)assay screens compounds that induce unfolding of a fluorescently taggedMfn2 construct. Note that both mini-peptides 1 and 2 influenced the FRETsignal, suggesting that they induced Mfn2 conformational changes (seee.g., Example 4).

FIG. 13 shows a multi-species alignment of MFN2 amino acid sequence.Black highlighting shows identity with human MFN2 protein.

FIG. 14 is a homology plot of MFN2 amino acid sequence by functionaldomain. Positions of HR1 MP374-384 (“fuse”) and its HR2 interacting site(“Binding”) are shown on exploded views below.

FIG. 15 is a series of images and a bar graph showing MFN2 Ser378 chargestatus determines fusion-promoting activity of HR1 MP374-384. Ser378substitution analysis of mitochondrial fusion promoted by HR1 MP374-384.Representative confocal images of MitoTracker Green/TMRE (red) stainedlive cells are on the left; scale bars are 10 μm. Group mean data fromFIG. 2D are to the right; p values are by ANOVA with Tukey's post hoccomparison.

FIG. 16A, FIG. 16B, FIG. 16C and FIG. 16D are a series of NMRspectroscopy images and calculated structures. NMR spectroscopy suggestsa structural mechanism for effects of Ser378 phosphorylation on HR1372-384 minipeptide fusogenic function. (A) Amide proton regions of 2DNOESY spectra of Ala371 to Arg384 fragment of hMFN2.left—unphosphorylated Ser378 peptide; right—peptide synthesized withphosphorylated Ser-378. Sequential cross peaks between amide groupsindicative of α-helical secondary structure are labeled. (B) Overlaid¹⁵N-¹H heteronuclear single quantum coherence spectra of minipeptidebackbone amides (bold highlights on covalent wire-model to the left).Red is Ser378 peptide; green is (p)-Ser378 peptide. # marks thepositions of Ser378 and (p)-Ser378. In addition to Ser378, the amidesignals for amino acids 379-382 shifted down-field (i.e. to highervalues) after phosphorylation, as observed when amides within peptidesform or strengthen hydrogen bonds. Here, phosphorylation of Ser378 caninduce hydrogen bonding for the amide of Leu379, stabilizing thedownstream helix and evoking the observed down-field shifts for amidesof His380 and Met381. (C) Ensembles of structures calculated from NMRrestraints. Color coding is the same as in (B). (D) PepFold3 modeling ofthe HR1 minipeptide shows how different backbone structure provoked bySer378 phosphorylation (see panel B) can alter Leu379 and His 380. * in(B) and (D) mark amino acids with the greatest changes between Ser378and (p)-Ser378 peptides.

FIG. 17 show calculated structures from the modeling of HR1 MP374-384conformation before (top) and after (bottom) S378 phosphorylation.

FIG. 18 shows mutagenesis analysis of MFN2-function based on Ser378phosphorylation status and integrity of Met376 and His380 that arespatially regulated by Ser378 phosphorylation. Group data andrepresentative confocal images showing mitochondrial aspect ratio inmitofusin deficient cells (MFN1−/−, MFN2−/− MEFs) infected with adnoviriexpressing β-galactosidase (negative control), wild-type (WT) MFN2(positive control), or different single amino acid MFN2 mutants.Fusogenic function was impaired in pseudo-phosphorylated MFN2 Ser378Asp(S378D) and alanine-substituted MFN2 Met376Ala (M376A) and His380Ala(H380A); non-phosphorylatable MFN2 Ser378Ala (S378A) and MFN2 Val372Ala(V372A, which is not in the HR1-HR2 interacting domain) retained fullactivity. p values are by ANOVA with Tukey's post hoc comparison. MEFswere stained as described in FIG. 15 legend. Scale bar is 10 μm.

FIG. 19A, FIG. 19B, FIG. 19C, FIG. 19D, and FIG. 19E are a series ofhigh-resolution tandem mass spectra of peptides from a tryptic digest ofPINK1-treated recombinant human MFN2. The spectra of the phosphopeptidewith the Ser-378 phosphorylation site (A), a stable isotope-labeledsynthetic phosphopeptide (B), and the non-phosphorylated peptide (C) areshown from a 4-hour in vitro PINK1 phosphorylation experiment. (D) and(E) are like (A) and (C) after an overnight period for PINK1phosphorylation. The m/z values for the assigned ions are highlighted inthe adjacent ion tables.

FIG. 20A and FIG. 20B are a series of high-resolution mass spectra ofPINK1-phosphorylated recombinant human MFN2 demonstratingphosphorylation of Thrill (A) and Ser442 (B). These spectra wereobtained in the study shown in FIGS. 19D and E. m/z values for assignedfragmentation ions are shown to the right.

FIG. 21A, FIG. 21B, and FIG. 21C are a series of high-resolution tandemmass spectra of peptides from tryptic digest of GRK-treated recombinanthuman MFN2. (A) Representative non-matching spectrum from the elutionwindow of the Ser-378 phosphopeptide. (B) Matching spectrum for thenon-phosphorylated peptide from the GRK tryptic digest. The m/z valuesfor the assigned ions are highlighted in the adjacent ion tables. (C)Retention time/m/z coordinates of tandem spectra that were analyzed bytargeted LC-MS for phosphorylation of the Ser-378 containing peptide.The seven tandem spectra that were acquired at retention times between82-83 min at m/z=446.542 showed no evidence of phosphorylation.

FIG. 22 is a series of representative live-cell confocal images and abar graph from studies described in FIG. 2H. Mitochondria of MFN1-/−,MFN2−/− MEFs infected with adenoviri expressing MFN2 mutants with orwithout adeno-PINK1 kinase were co-stained with MitoTracker Green(green) and TMRE (red); nuclei are stained blue with Hoechst. Scale barsare 10 μm. Quantitative group mean data to the right are reproduced fromFIG. 2H for comparison.

FIG. 23 is a series of images and a bar graph showing effects of MFN2mutations that prevent or mimic Ser378 phosphorylation on mitochondrialfusion measured as content exchange. (left) Representative live cellconfocal images showing mitochondrial fusion (red/green mixing) 3 hoursafter PEG treatment of MFN1−/−, MFN2−/− MEFs expressing MFN2 Ser378mutants. Scale bar is 21 μm. N=3 independent studies; p values are byANOVA with Tukey's post hoc comparison.

FIG. 24A and FIG. 24B show functional screening for fusogenic activityof mitofusin agonist pharmacophores. (A) Mitochondrial fusogenicitymeasured as aspect ratio of MFN2 null MEFs after overnight treatmentwith 1 mM indicated library compound. Chemical details, structures, andcommercial sources of these compounds are in TABLE 4. Mock=DMSO vehiclecontrol. Horizontal dotted line indicates baseline value. Cells treatedwith 5 mM mitofusin agonist peptide HR1 367-384 (positive control) hadaspect ratios of ˜6. Inset: correlation of rank order for initial modelfit vs actual fusogenicity (r=0.214). Red dots are compounds A10 and B1that ranked 4^(th) and 2^(nd) for fusogenicity, but 22^(nd) and 31^(st),respectively, for fit to the original pharmacophore model. (B)Cytotoxicity measured by live-dead assay. Compounds are ranked byfusogenicity as in A. Means±SEM of 3 independent experiments examining˜30 cells per experiment.

FIG. 25A, FIG. 25B, and FIG. 25C shows functional validation anddose-response relations of candidate fusogenic small molecules. (A)Chemical structures of 4 top candidate fusogenic compounds from initialscreening (see e.g., FIG. 24). (B) Dose relations with representativeimages of vehicle and 1 mM treated Mfn2 null MEFs for each of thecompounds, only 3 of which were true positives. Cells are stained withMitotracker orange, calcein AM (green; alive) and ethidium homodimer(red nucleus; dead). There are no dead cells. EC₅₀ values are providedfor true positives; D9 showed no true fusogenic activity. Scale bars are10 microns. Dose-response curves are means±SEM of 3 independentexperiments. (C) Schematic depiction of pharmacophore model fit for the3 true positive fusogenic compounds.

FIG. 26 is a graph and image showing the synergistic effects of a classA and class B mitofusin agonist. Mitochondrial elongation (increase inaspect ratio) in MFN2-deficient MEFs stimulated by equimolarconcentrations of mitofusin agonists A and B. Dose-response curve on theleft is from 6 independent experiments. Peak aspect ratio achieved withA+B is ˜25% greater than with either agonist alone (compare to SF10C).Representative live-cell confocal images are on right. Scale bar is 10mm.

FIG. 27 is a series of graphs and an image showing the functionalevaluation of structurally diverse mitofusin agonists. (A) Mitochondrialelongation stimulated by mitofusin agonists A and B or chimera B-A/I incells having different MFN expression profiles. White bars are vehicle(DMSO) treated, black bars are 1 μM agonist overnight; *=p<0.05 vsvehicle (t-test). (B) Effects of cpds A and B or chimera B-A/I (1 μM) ondynamin-mediated endocytosis of Alexa-Fluor 594 Dextran. Dynasore is adynamin inhibitor. (C) Cell viability assessed after overnight exposureto indicated concentrations of mitofusin agonist (n=4). Test compoundswere not fully soluble at concentrations greater than 50 μM. p valuesare by ANOVA with Tukey's test.

FIG. 28A, FIG. 28B, FIG. 28C, FIG. 28D, FIG. 28E, FIG. 28F and FIG. 28Gare a series of graphs and images showing mitofusin agonists restoreaxonal mitochondrial trafficking suppressed by CMT2A mutant MFN2 T105M.(A-C) Chimera B-A/I effects on mitochondrial mobility (A), function (B),and morphology (C) in cultured CMT2A MFN2 T105M mouse neurons. (D)Kymograph of mitochondrial trafficking in a Ctrl mouse sciatic nerve.(E) Serial kymographs of mitochondria in a MFN2 T105M mouse sciaticnerve before and after chimera B-A/I. (F) Quantitative data for sciaticnerve mitochondrial motility studies. (G) Size of motile and staticmitochondria in Ctrl and B-A/I-treated (60 minutes) sciatic nerves. Datainformation: Mean, standard deviation, and P-values calculated usingtwo-tailed t-test are shown. MitoSOX n=4, TMRM n=6, Mito Aspect ration=4.

FIG. 29 shows in vitro mouse mitochondrial mobility in Ctrl neuron, MFN2T105M neuron, and MFN2 T105M neuron treated with compounds A+B (24hours).

FIG. 30 is a series of images showing mitofusin agonist chimera B-A/Ireverses mitochondrial abnormalities induced by CMT2A mutant MFN2 T105Min cultured mouse neurons. Representative confocal images of livingmouse neurons expressing MitoGFP and stained with TMRE and Hoescht fromexperiments reported in FIG. 28B and FIG. 28C. Scale bars are 21 μm;expanded views are from white squares. MFN2 T105M was induced byaddition of adeno-Cre.

FIG. 31 shows mitochondrial mobility in a neuronal axon of a controlmouse sciatic nerve. Blue arrows represent the mitochondrial transportin the nerve.

FIG. 32 shows mitochondrial mobility in axons of a MFN2 T105M mousesciatic nerve before and at serial 15 minute periods after applicationof chimera B-A/I. Blue arrows represent the mitochondrial transport inthe nerve.

FIG. 33 shows the synthetic route for preparation of Chimera B-A/I(compound 5).

FIG. 34A and FIG. 34B show RP-HPLC and HRMS of newly synthesized chimeraB-A/I. (A) HPLC spectrum of chimera B-A/I. From top to bottom: UVAbsorbance at 215 nm; UV Absorbance at 254 nm; complete ionization massselective detector (MSD) spectrum; evaporative light scatteringdetection spectrum. Chimera B-A/I was 99.99% pure. (B) HRMS chromatogramof compound B-A/I (C21H29N5OS) shows exact mass: [M+H]⁺: 400.2.

FIG. 35A and FIG. 35B show the proton and carbon-13 NMR of newlysynthesized chimera B-A/I. (A) Full ¹H NMR spectrum (400 MHz) ofcompound B-A/I (DMSO-d₆ solvent) and expanded view of region δ 0.0-4.0PPM. (B) ¹³C NMR spectrum (126 MHz) of compound B-A/I (CDCl₃ solvent).

FIG. 36 shows the synthetic route for preparation of chimera B-A/s(compound 3).

FIG. 37A and FIG. 37B show RP-HPLC and HRMS of newly synthesized chimeraB-A/s. (A) HPLC spectrum of compound B-A/s. From top to bottom: UVAbsorbance at 215 nm; UV Absorbance at 254 nm; complete ionization MSDspectrum; evaporative light scattering detection spectrum. Chimera B-A/swas 99.99% pure. (B) HRMS chromatogram of compound B-A/s (C21H28N4OS)shows exact mass found: [M+H]⁺: 385.2.

FIG. 38A and FIG. 38B show the proton and carbon-13 NMR of newlysynthesized chimera B-A/s. (A) Full ¹H NMR spectrum (500 MHz) ofcompound B-A/s (DMSO-d₆ solvent) and expanded view of region 60.5-4.8PPM. (B) ¹³C NMR spectrum (126 MHz) of compound B-A/s (DMSO-d₆ solvent)and expanded view of region δ 5-60 PPM.

FIG. 39 shows the synthetic route for preparation of chimera A-B/I(compound 5).

FIG. 40A and FIG. 40B show RP-HPLC and HRMS of newly synthesized chimeraA-B/I. (A) HPLC spectrum of newly synthesized chimera A-B/I. From top tobottom: UV Absorbance at 215 nm; UV Absorbance at 254 nm; completeionization MSD spectrum; evaporative light scattering detectionspectrum. Chimera A-B/I was 97.56% pure. (B) HRMS chromatogram ofcompound A-B/I (C18H21N3O2S2) shows exact mass found: [M+H]⁺: 376.0.

FIG. 41A and FIG. 41B show Proton and carbon-13 NMR of newly synthesizedchimera A-B/I. (A) Full ¹H NMR spectrum (400 MHz) of newly synthesizedchimera A-B/I (DMSO-d₆ solvent) and expanded view of region δ 2.0-4.1PPM. (B) ¹³C NMR spectrum (126 MHz) of chimera A-B/I (DMSO solvent).

FIG. 42 is a schematic showing the synthetic route for preparation ofchimera A-B/s (compound 3).

FIG. 43A and FIG. 43B show RP-HPLC and HRMS of newly synthesized chimeraA-B/s. (A) HPLC spectrum of compound A-B/s. From top to bottom: UVAbsorbance at 215 nm; UV Absorbance at 254 nm; complete ionization MSDspectrum; evaporative light scattering detection spectrum. Chimera A-B/swas 98.76% pure. (B) HRMS chromatogram of chimera A-B/s (C18H20N2O2S2)shows exact mass found: [M+H]⁺: 361.2.

FIG. 44A and FIG. 44B show the proton and carbon-13 NMR spectra of newlysynthesized chimera A-B/s. (A) Full ¹H NMR spectrum (400 MHz) of chimeraA-B/s (DMSO-d₆ solvent) and expanded view of region δ 5.7-8.2 PPM. (B)¹³C NMR spectrum (126 MHz) of chimera A-B/s (DMSO-d₆ solvent).

FIG. 45 shows the initial PK studies of Chimera B-A/I, a.k.a.Regeneurin-S. In vitro pharmacokinetic profiling of Regeneurin-S revealsrapid degradation by liver mcirosomes. Chimera B-A/I from Rocha, et alScience 2018 was designated Regeneurin-S. Shown is its chemicalstructure and results of three independent pharmacokinetic (PK) assaysperformed months apart.

FIG. 46 is a series of structures showing structural considerations forchemical evolution of the lead mitofusin agonist. (top left) Structuralmodel of human Mfn2 HR1 367-384 agonist peptide (ribbon) in context ofMfn2 HR1 domain from which it was derived (space-filling; from FrancoNature 2016); side chains of HR1-HR2 interacting amino acids Val372,Met376, and His380 are depicted. (top right) Structure of HR1 367-384peptidomimetic Regeneurin-S (chimera B-A/I from Rocha Science 2018) isshown mimicking function-critical side chains from HR1 367-384. Modeledusing Chimera UCSF. (bottom) Functional groups of Regeneurin-S aredepicted as conceived for chemical engineering: methylated cyclohexylcorresponding to ring structure of His380; thioether backbone providingproper spacing; phenyl-, cyclopropyl-substituted triazol ring mimickinghydrophobicity of Met376 and Val372.

FIG. 47 is a series of structures and a graph showing backbone sulfurmodifications or substitutions do not alter Regeneurin mitofusin agonistefficacy or affect its degradation by liver microsomes. The backbonesulfur of the parent thioether was oxidized using hydrogen peroxide togenerate the sulfoxide and sulfone, which are potential metabolites(top). The ether and carbon variants and carbon variant withtetrahydropyran substituted for methylated cyclohexane were synthesizedde novo (bottom). Red rectangles show substitutions. T % is for humanliver microsomes, % bound is for human plasma. (All PK studies were notperformed on all backbone variants.) Dose-response curves formitochondrial elongation (bottom left) are similar for all compounds.

FIG. 48 is a bar graph and a series of structures showing functionalscreening of commercially available Cpd B triazol ring substitutionvariants. Top: Rank order of fusogenicity (increase in mitochondrialaspect ratio of Mfn2 null MEFs in response to 1 mM compound overnight)provoked by compounds in Supplemental dataset 1. Red dashed lineindicates baseline aspect ratio (DMSO-treated MEFs, negative control);green dashed line shows aspect ratio in response to Cpd B (positivecontrol). Bottom: Triazol ring substitutions of 17 compounds otherwisehaving the common structure R_((B)). Cpd B is indicated with redrectangle; the other four fusogenic compounds are indicated with greenrectangles. Results of detailed studies of these compounds are in FIG.49.

FIG. 49 is a series of structures and a graph showing dose-response andhuman liver microsomal stability data for fusogenic compounds from FIG.22. EC₅₀ values are mean±SEM of 3 independent experiments assessingmitochondrial aspect ratio in Mfn2 null MEFs; Group data dose-responsecurves are on the left. T_(1/2) values are from human liver microsomestability assay.

FIG. 50 is a series of structures and a graph showing a mitolityn seriesof mitofusin agonists. The feature that distinguishes Mitolityns fromRegeneurins is replacement of the 2-phenyl group on the 2,4,5 triazolring with ethyl or methyl groups. Mitolityns 1 and 2 are 2-ethylcyclohexane variants and Mitolityns 3 and 4 are 2-ethyl tetrahydropyranvariants; Mitolityns 5 and 6 are like 3 and 4 with 2-methyl rather than2-ethyl groups off the 2,4,5 triazol ring. Chemical differences fromMitolityn-1 are shown in red rectangles; molecular weights are inparentheses. EC₅₀ values are for stimulated increase in mitochondrialaspect ratio in Mfn2 null MEFs (n=3 each, mean±SEM); T_(1/2) values arefor human, rat, and mouse liver microsome stability assay, in thatorder. % bound is for human plasma. Group mitochondrial aspect ratiodose response data are shown at the bottom. Mitolityns-4 and -6exhibited highest potency in the fusogenicity assay, stability in theliver microsome assay, and low plasma protein binding.

FIG. 51 shows dose-dependent mitochondrial fusion without cytotoxicityof structurally diverse mitofusin agonists. At the top are depictions ofMitolityn-4 (left) and Regeneurin-C (right) mimicry of function-criticalside chains of parent agonist peptide Mfn2 HR1 367-384. At the bottomare dose-response relations for each agonist: circles/solid lines showfusogenic responses (mitochondrial elongation assay); squares/dashedlines show % dead cells assayed using the Live-Dead stain. Mfn2 nullMEFs were treated with compounds overnight. Indicated EC₅₀ values aremean±SEM, n=3 each.

FIG. 52 shows the results of in vitro pharmacokinetic studies ofRegeneurin-C, Regeneurin-C/O, and Mitolityn-4 mitofusin agonists.

FIG. 53A and FIG. 53B are a series of graphs and correspondingstructures showing in vivo pharmacokinetics of Regeneurin-C, RegeneurinC/O and Mitolityn-4. (A) Three mice each were administered 1 mg/kgagonist IV, IP, or IM. Graphs are mean plasma concentration for eachadministration route. (B) Results for individual mice were administered1 mg/kg indicated agonist IM.

FIG. 54 is a series of structures describing the ongoing chemicalmodifications and optimizations of Regeneurin C/O.

FIG. 55 is a series of structures of the Fusogenin series of Mfnagonists currently being synthesized.

FIG. 56 is a series of graphs describing Regeneurin-C (100 nM overnight)treatment of primary fibroblasts from human patients with geneticallydiverse neurodegenerative diseases. FCCP treatment shows effects ofcomplete mitochondrial uncoupling. Ctrl are control primary humanfibroblasts.

FIG. 57A, FIG. 57B, FIG. 57C and FIG. 57D are an illustration, traces,and bar graphs describing the initial phenotyping studies of CMT2A mouse(Mfn2 T105M flox-stop×H9B Cre). (A) Schematic depiction of nerveconduction studies; red arrows show positions of stimulating electrodes,blue arrows of sensing electrodes. (B) Representative CMAP tracings fromnormal control (top) and CMT2A Mfn2 T105M (bottom) mice. Posteriortibial tracings control for CMAP sensing, and are no different asexpected. Note marked decrease in amplitude of Sciatic nerve tracing inT105M mouse. (C) Group data from ongoing CMAP studies; each n is amouse. CMAP amplitude, but not conduction velocity (latency/length) isdiminished after 20 weeks in CMT2A mice. (D) Group data from ongoingRotarod studies suggest functional decline between 10 and 20 weeks.

FIG. 58 is a series of images and a graph showing Regeneurin-C/Ocorrects CMT2A neuronal mitochondrial dymotility in vivo. 10 week oldCMT2A MFN2 T105M mice were injected IM with Mfn agonist Regeneurin-C/O 2mg/kg twice, or vehicle. Sciatic nerve mitochondrial motility wasmeasured 4 hours later. Results for 2 CMT2A mice per group.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure is based, at least in part, on the discovery thatmodeling mini peptides can provide small molecule regulators ofmitochondrial fusion for use in treating mitochondrial associateddiseases, disorders, and conditions. As shown herein, the presentdisclosure provides new compositions, uses, and techniques forregulating mitochondrial function, including mitochondrial tracking andfusion. These compositions and methods can be useful to correct cell andorgan dysfunction caused by primary abnormalities in mitochondrialfission, fusion and subcellular motility/distribution.

As described herein, novel small molecules were designed thatincorporated functional features (e.g., potency, specificity) of twomitofusin agonist peptidomimetic compounds identified from a functionalscreen (Cpds A and B) which were functionally synergistic because theyacted on different phosphorylated forms of MFN (see e.g., Example 2).

As described herein, the discovery that“super-activating”/“turbocharging” the endogenous normal mitofusins tooverwhelm dominant inhibition by mutant mitofusins constitutes a novelapproach to treating diseases caused by loss of function MFN2 mutations.Not only was (1) a way to pharmacologically stimulate mitofusin activity(e.g., fusion and trafficking) discovered, but (2) a therapeuticapproach was also designed that bypasses effects of the mutant Mfn2 inCMT2A. This makes the approach applicable no matter the nature of apatient's individual mutation. As such, this approach is better than“personalized medicine”; this approach can be used to treat anyindividual with any mitofusin mutation.

Conventional wisdom is that unopposed mitochondrial fission (resultingin small mitochondrial size) is primarily responsible for disease (e.g.,as in Charcot Marie Tooth Disease). But the present disclosure providesfor the surprising discovery that, mitochondrial transport, notmitochondria size, is a more important causative factor in disease stateand progression. As described herein, it was discovered thatmitochondrial trafficking (e.g., the ability for mitochondria to getfrom point A to point B) is responsible (see e.g., Example 5).

The present disclosure shows that pharmacological disruption ofintramolecular restraints in MFN2 enhances mitochondrial fusion andtrafficking in CMT2A neurons. Mitofusins (MFNs) promote fusion-mediatedmitochondrial content exchange and subcellular trafficking. DamagingMfn2 gene mutations cause neurodegenerative Charcot Marie Tooth Diseasetype 2A (CMT2A). Here it has been shown that Mfn2 activity is determinedby Met376 and His380 interactions with Asp725 and Leu727 and controlledby PINK1 kinase-mediated phosphorylation of adjacent Mfn2 Ser378. Alsoshown here, are small molecule mimics of the peptide-peptide interfacedisrupted this interaction, allosterically activating Mfn2 and promotingmitochondrial fusion. These first-in-class mitofusin agonists overcamedominant mitochondrial defects provoked in cultured neurons by CMT2Amutants Mfn2 Arg94Gln and Thr105Met, as evidenced by improvedmitochondrial dysmotility, fragmentation, depolarization, and clumping.Mitofusin agonists normalized axonal mitochondrial trafficking withinsciatic nerves of Mfn2 Thr105Met mice, promising a therapeutic approachfor CMT2A and other untreatable diseases of impaired neuronalmitochondrial dynamism or trafficking.

As described herein (see e.g., Example 5), based on molecular modelingand a detailed structural and functional interrogation of MFN2-derivedminipeptides encompassing Met³⁷⁶, Ser³⁷⁸, and His³⁸⁰ small moleculemitofusin agonists were developed that reversed mitochondrialdysmorphometry and normalized impaired mobility evoked by 2 CMT2A MFN2mutants. CMT2A is the prototypical clinical disorder of defectivemitochondrial fusion, but impaired mitochondrial trafficking may play asgreat a role as mitochondrial fragmentation in CMT2A axonaldegeneration. Individuals with CMT2A express one mutant MFN2 allele incombination with one normal MFN2 allele and harbor two normal MFN1alleles. As such, it has been shown herein that it is possible that atherapeutic substrate for agonists to “supercharge” normal mitofusinsand overcome dominant inhibition by MFN2 mutants. As shown herein, invivo mitochondrial dysmotility (provoked by CMT2A mutants), normalizedby mitofusin agonists, mechanistically links abnormal mitochondrialtrafficking in CMT2A to MFN2 dysfunction. Mitofusin agonists may alsohave therapeutic potential for neurological conditions other than CMT2A,such as Alzheimer's, Parkinson's, and Huntington's diseases, whereinmitochondrial dysmotility and fragmentation are contributing factors.

Mitofusin Modulating Agent

The present disclosure provides for small molecule mimics of a Mfn2peptide-peptide interface. As described herein, a composition for thetreatment of a mitochondria-associated disease, disorder, or condition,can comprise a mitofusin modulating agent, such as a peptide mimetic(e.g., a small-molecule peptide mimetic). A peptide mimetic can be achemical peptide mimetic. For example, the peptide mimetic can mimic amitofusin peptide.

As described herein, chemical peptido-mimetics were identified, andsecond generation small molecules were designed, based on structuralmodeling of functionally-critical amino acid side chains of mitofusin(Mfn)-derived mini-peptides (mini-peptides described in Franco et al.Nature 2016). These peptide mimetic compounds activate mitochondrialfusion by directing Mfn1 and Mfn2 to different conformational states. Itis believed that these are the first small molecules to target Mfn1 orMfn2. Specific combinations of small molecules that activatemitochondrial trafficking and mitochondrial fusion, and their use tocorrect mitochondrial and cellular dysfunction, are described herein.

As described herein, mitofusin modulating agents (e.g., mitofusinagonists) can reverse mitochondrial defects. For example, mitofusinmodulating agents can also have mitochondria transport activity. Asanother example, a mitofusin modulating agent can modulate or enhancethe transport (e.g., trafficking, mobility, or movement) ofmitochondria, in for example, a nerve. Example 5 shows that mitofusinagonists restore axonal mitochondrial trafficking (see e.g., FIG. 28).Also described herein, mitofusin agonists enhance mitochondrialelongation or mitochondrial elongation aspect ratio. Examples furthershow, pharmacological disruption of intramolecular restraints in Mfn2 bymitofusin modulating agents promotes mitochondrial fusion andtrafficking in neurons.

As described herein, the mitofusin modulating agents can increasemitochondrial trafficking without affecting or substantially affectingmitochondrial fusion or fission.

Mitofusin Mini Peptide

As described herein, a peptide mimetic can be a mitofusin mini-peptideas described in U.S. Provisional Patent Application 62/397,110(incorporated herein by reference) filed Sep. 20, 2016 and Franco et al.Nature 2016.

Mfn Agonist (Fusion-Promoting) Peptido-Mimetic

As described herein, a peptide mimetic can be a Mfn agonist(fusion-promoting) peptido-mimetic that competes with endogenous HR1-HR2binding.

The Mfn agonist was designed based on the discovery that Mfn1 and Mfn2share a common domain structure and structural homology with human Mfn1and Arabidopsis thaliana dynamin-related protein. As described herein,Mfn1 and Mfn2 share a common domain structure that was modeled withI-TASSER and structural homology with bacterial dynamin-like protein,human Mfn1 and Arabidopsis thaliana dynamin-related protein (see e.g.,FIG. 1). The model shows how the first heptad repeat domain (HR1)interacts in an anti-parallel manner with the carboxyl terminal secondheptad repeat (HR2) domain to restrain it and prevent its extension intothe cytosol, which is currently believed to be necessary formitochondrial tethering and fusion (see e.g., Example 1).

As described herein, an Mfn agonist can inhibit or block HR1-HR2 bindingor interaction. For example, Met376, Ser378, His380, or Met 381 aminoacids were discovered to be necessary for the HR1-HR2 interaction. Aminoacids implicated in HR1-HR2 binding or interactions were identified byfirst defining a minimal HR1-derived mini-peptide that competes withendogenous HR1-HR2 binding (see e.g., FIG. 2A-FIG. 2B), followed byfunctional analyses of a complete series of alanine substituted peptides(see e.g., FIG. 2C). Based on these results chemical peptido-mimeticswere derived that, by mimicking the 3-dimensional spatial and chargecharacteristics of these critical amino acid side chains, have similarmodulatory activity on mitochondrial fusion as the N-terminalmini-peptide (see e.g., Example 1).

Novel Regeneurin agonists (see Example 6, TABLE 8) are described below.

Compound ID IUPAC Name Structure M.W. (g/mol) Formula Regeneurin-C1-(3-(5- cyclopropyl-4- phenyl-4H-1,2,4- triazol-3- methylcyclohexyl)urea

381.52 C₂₂H₃₁N₅O Regeneurin-O 1-(2-((5- cyclopropyl-4- phenyl-4H-1,2,4-triazol-3- yl)oxy)ethyl)-3-(2- methylcyclohexyl) urea

383.49 C₂₁H₂₉N₅O₂ Regeneurin-C/O 1-(3-(5- cyclopropyl-4-phenyl-4H-1,2,4- triazol-3- yl)propyl)-3- (tetrahydro-2H-pyran-4-yl)urea

369.47 C₂₀H₂₇N₅O₂ Regeneurin-SO 1-(2-((5- cyclopropyl-4-phenyl-4H-1,2,4- triazol-3- yl)sulfinyl)ethyl)-3- (2- methylcyclohexyl)urea

415.55 C₂₁H₂₉N₅O₂S Regeneurin-SO₂ 1-(2-((5- cyclopropyl-4-phenyl-4H-1,2,4- triazol-3- yl)sulfonyl)ethyl)- 3-(2- methylcyclohexyl)urea

431.56 C₂₁H₂₉N₅O₃S

Novel Mitolityn agonists (see Example 6, TABLE 9) are described below.

Compound ID IUPAC Name Structure M.W. (g/mol) Formula Mitolityn-11-(3-(5-cyclopropyl- 4-ethyl-4H-1,2,4- triazol-3-yl)propyl)- 3-(2-methylcyclohexyl) urea

333.47 C₁₈H₃₁N₅O Mitolityn-2 1-cyclohexyl-3-(3- (5-cyclopropyl)-4-ethyl-4H-1,2,4- triazol-3- yl)propyl)urea

319.45 C₁₇H₂₉N₅O Mitolityn-3 1-(3-(5-cyclopropyl- 4-ethyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(3- methyltetrahydro- 2H-pyran-4-yl)urea

335.44 C₁₇H₂₉N₅O₂ Mitolityn-4 1-(3-(5-cyclopropyl- 4-ethyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(tetrahydro-2H- pyran-4-yl)urea

321.42 C₁₆H₂₇N₅O₂ Mitolityn-5 (Renamed Fusogenin- 4a)1-(3-(5-cyclopropyl- 4-methyl-4H-1,2,4- triazol-3-yl)propyl)-methyltetrahydro- 2H-pyran-4-yl)urea

321.43 C₁₆H₂₇N₅O₂ Mitolityn-6 (Renamed after Fusogenin- 3a)1-(3-(5-cyclopropyl- 4-methyl-4H-1,2,4- triazol-3-yl)propyl)-3-(tetrahydro-2H- pyran-4-yl)urea

307.4 C₁₅H₂₅N₅O₂

Novel Fusogenin agonists (see Example 6, TABLE 10) are described below.

Compound ID IUPAC Name Structure M.W. (g/mol) Formula Fusogenin-11-(3-(4-methyl-5- phenyl-4H-1,2,4- triazol-3-yl)propyl)- 3-(2-methylcyclohexyl)- urea

355.49 C₂₀H₂₉N₅O Fusogenin-3 1-(3-(4-methyl-5- phenyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(tetrahydro-2H- pyran-4-yl)urea

343.43 C₁₈H₂₅N₅O₂ Fusogenin-4 1-(3-(4-methyl-5- phenyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(3- methyltetrahydro- 2H-pyran-4-yl)urea

357.46 C₁₉H₂₇N₅O₂

Mitofusin Modulating Agents: Small Molecules to Target Mfn1 and/or Mfn2

The small molecule Mfn regulators as described herein are allostericagonists. An agonist can be a substance that fully activates thereceptor that it binds to, and an antagonist can be a substance thatbinds to a receptor but does not activate and can block the activity ofother agonists.

Examples of mitofusin modulating agents are described herein (see e.g.,Example 2). Mitofusin modulating agents can be, of the formula:

or a pharmaceutically acceptable salt, tautomer, or stereoisomer thereofwherein,

R¹ is selected from the group consisting of C₁₋₈ alkyl, C₁₋₈ alkylsubstituted with S, S, thiophene, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, thiophene, and thiophene carboxamide;

R² is selected from the group consisting of C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, imidazole, thiophene, thiophenecarboxamide, and triazole;

R³ is selected from the group consisting of hydrogen (H) and C₁₋₈ alkyl;

R⁴ is selected form the group consisting of hydrogen (H) and C₁₋₈ alkyl;

R⁵ is selected from the group consisting of C₁₋₈ alkyl, C₁₋₈ alkylsubstituted with S, S, thiophene, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, thiophene, thiophene carboxamide, and triazole;

R⁶ is selected from the group consisting of bicyclononanone, pyrrole,benzimidizole, pyrrole substituted pyrrole, and substitutedbenzimidizole;

R⁷ is selected from the group consisting of C₁₋₈ alkyl, pyrrole, pyrrolesubstituted pyrrole, benzimidizole, and substituted benzimidizole;

R⁸ is selected from the group consisting of hydrogen (H);

R⁹ is selected from the group consisting of C₁₋₈ alkyl; pyrrole,substituted pyrrole, pyrrole substituted pyrrole, benzimidizole, andsubstituted benzimidizole;

X is selected from the group consisting of O, C, and N;

Y is selected from the group consisting of O, C, and N; and

Z is a linker group selected from the group consisting of a bond or C₁₋₆alkyl; and

optionally, R¹ and R² form a cyclic group, R¹ and R⁴ form a cyclicgroup, R² and R³ form a cyclic group, R⁴ and R³ form a cyclic group; orR⁸ and R⁷ form a cyclic group,

wherein,

the bicyclononanone optionally comprises one or more N atoms.

Optionally, the compound of formula (I), (II), or (Ill) is not acompound of TABLE 4, TABLE 5, TABLE 7, or the commercially sourcedcompositions in TABLE 1 or TABLE 2.

Furthermore, R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, or R⁹ can be optionallysubstituted by one or more of acetamide, C₁₋₈ alkoxy, amino, azo, Br,C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O,phenyl, S, sulfoxide, sulfur dioxide, or thiophene and optionallyfurther substituted with acetamide, alkoxy, amino, azo, Br, C₁₋₈ alkyl,carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O, phenyl, S,sulfoxide, sulfur dioxide, or thiophene and the alkyl, cycloalkyl,heteroaryl, heterocyclyl, indole, or phenyl is optionally furthersubstituted with one or more selected from the group consisting ofacetamide, alkoxy, amino, azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl,cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F,halo, indole, N, nitrile, O, phenyl, S, sulfoxide, or thiophene.

The R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, or R⁹ groups can be optionallysubstituted or further substituted with one or more groups independentlyselected from the group consisting of hydroxyl; C₁₋₁₀ alkyl hydroxyl;amine; C₁₋₁₀ carboxylic acid; C₁₋₁₀ carboxyl; straight chain or branchedC₁₋₁₀ alkyl, optionally containing unsaturation; a C₂₋₈ cycloalkyloptionally containing unsaturation or one oxygen or nitrogen atom;straight chain or branched C₁₋₁₀ alkyl amine; heterocyclyl; heterocyclicamine; and aryl comprising a phenyl; heteroaryl containing from 1 to 4N, O, or S atoms; unsubstituted phenyl ring; substituted phenyl ring;unsubstituted heterocyclyl; and substituted heterocyclyl, wherein theunsubstituted phenyl ring or substituted phenyl ring can be optionallysubstituted with one or more groups independently selected from thegroup consisting of hydroxyl; C₁₋₁₀ alkyl hydroxyl; amine; C₁₋₁₀carboxylic acid; C₁₋₁₀ carboxyl; straight chain or branched C₁₋₁₀ alkyl,optionally containing unsaturation; straight chain or branched C₁₋₁₀alkyl amine, optionally containing unsaturation; a C₂₋₁₀cycloalkyloptionally containing unsaturation or one oxygen or nitrogen atom;straight chain or branched C₁₋₁₀ alkyl amine; heterocyclyl; heterocyclicamine; aryl comprising a phenyl; and heteroaryl containing from 1 to 4N, O, or S atoms; and the unsubstituted heterocyclyl or substitutedheterocyclyl can be optionally substituted with one or more groupsindependently selected from the group consisting of hydroxyl; C₁₋₁₀alkyl hydroxyl; amine; C₁₋₁₀ carboxylic acid; C₁₋₁₀ carboxyl; straightchain or branched C₁₋₁₀ alkyl, optionally containing unsaturation;straight chain or branched C₁₋₁₀ alkyl amine, optionally containingunsaturation; a C₂₋₈ cycloalkyl optionally containing unsaturation orone oxygen or nitrogen atom; heterocyclyl; straight chain or branchedC₁₋₁₀ alkyl amine; heterocyclic amine; and aryl comprising a phenyl; andheteroaryl containing from 1 to 4 N, O, or S atoms. Any of the above canbe further optionally substituted.

In some embodiments, R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, or R⁹ areoptionally substituted by one or more of: acetamide, alkoxy, amino, azo,Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O,phenyl, S, sulfoxide, sulfur dioxide, or thiophene; and optionallyfurther substituted with one or more acetamide, alkoxy, amino, azo, Br,C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O,phenyl, S, sulfoxide, sulfur dioxide, or thiophene; wherein the alkyl,cycloalkyl, heteroaryl, heterocyclyl, indole, or phenyl, is optionallyfurther substituted with one or more of acetamide, alkoxy, amino, azo,Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, N, nitrile, O,phenyl, S, sulfoxide, sulfur dioxide, or thiophene.

In some embodiments, mitofusin modulating agent or agonists can beselected from the compounds below or the R¹, R², R³, R⁴, or R⁵ groups orX or Y comprised in the below compounds can be selected independentlyand placed into formula (I), (II), or (Ill) (see e.g., TABLE 7, 70commercially available compounds):

TABLE 7 70 commercially available compounds % long compare 1-A01 to BPosition Structure Name 202 1-F9

2-(2-{[5-cyclopropyl- 4-(prop-2-en-1-yl)- 4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7- tetrahydro-1- benzothiophene-3-carboxamide 141 1-G1

2-(2-{[4-(2- methylphenyl)-5- (pyridin-3-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide128 1-D2

2-(2-{[4-(4- methoxyphenyl)-4H- 1,2,4-triazol-3- yl]sulfanyl}acetamido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 114 D08

2-{[(3aS,6aS)-5- {5,7- dimethylpyrazolo[1,5- a]pyrimidine-2- carbonyl}-octahydropyrrolo[3,4- b]pyrrol-1- yl]methyl}-1-methyl- 1H-imidazole 1071-B1

2-{2-[(4-methyl-5- phenyl-4H-1,2,4- triazol-3- yl)sulfanyl]acetamido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 105 1-D4

N-benzyl-2-(2- {5H,6H,7H,8H,9H- [1,2,4]triazolo[4,3- a]azepin-3-ylsulfanyl}acetamido)- 4,5,6,7-tetrahydro- 1-benzothiophene-3-carboxamide 100 B01

2-{2-[(5-cyclopropyl- 4-phenyl-4H-1,2,4- triazol-3- yl)sulfanyl]propana-mido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 99 1-G11

2-{2-[(5-cyclopropyl- 4-ethyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide92 1-D7

2-[2-({4-[(furan-2- yl)methyl]-5-phenyl- 4H-1,2,4-triazol-3-yl}sulfanyl)propana- mido]-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 90 1-B3

2-{2-[(5-cyclopropyl- 4-phenyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide75 A4

3-(4-methylphenyl)- 1-(4- phenylbutyl)urea 73 D09

3-{[2-(1H-1,3- benzodiazol-2- yl)ethyl]sulfanyl}-1-(3-fluorophenyl)pyrro- lidine-2,5-dione 71 A10

1-[2-(benzylsulfanyl)ethyl]- 3-(2-methylcyclohexyl)urea 68 1-B6

2-{2-[(5-cyclopropyl- 4-methyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- N-(2-methoxyethyl)- 4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide 64 B07

2-[(tert- butylcarbamoyl)amino]- 2-oxoethyl 2- [({4-oxo-5-phenyl-3H,4H-thieno[2,3- d]pyrimidin-2- yl}methyl)sulfanyl] acetate 59 pA

3-phenyl-1-(4- phenylbutyl)urea 55 A09

2-{[4-benzyl-5- (morpholin-4-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}-N-(2,3- dihydro-1,4- benzodioxin-6- yl)propanamide 47 A08

2-({2-[(morpholin-4- yl)methyl]quinazolin- 4-yl}sulfanyl)-N-[3-(trifluoromethyl)- phenyl]propanamide 47 1-A8

2-{2-[(5-benzyl-4- ethyl-4H-1,2,4- triazol-3- yl)sulfanyl]propana-mido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 45 1-A10

2-(2- {5H,6H,7H,8H,9H- [1,2,4]triazolo[4,3- a]azepin-3-ylsulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide41 1-B7

2-[2-({4-methyl-5- [(thiophen-2- yl)methyl]-4H-1,2,4- triazol-3-yl}sulfanyl)propana- mido]-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 39 1-C10

methyl 2-{2-[(5- methyl-4-phenyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxylate39 B03

2-{[4-benzyl-5- (morpholin-4-yl)-4H- 1,2,4-triazol-3- yl]sulfanyl}-N-(2-oxo-2,3-dihydro-1H- 1,3-benzodiazol-5- yl)propanamide 38 1-E1

2-(2-{[5-cyclohexyl- 4-(prop-2-en-1-yl)- 4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide36 B09

N-(2-{[(5- bromothiophen-2- yl)methyl]sulfanyl}- ethyl)-1-(thiophene-2-carbonyl)piperidine- 3-carboxamide 35 1-C8

2-[2-({4-phenyl-5- [(thiophen-2- yl)methyl]-4H-1,2,4- triazol-3-yl}sulfanyl)acetamido]- 4H,5H,6H- cyclopenta[b]Ihiophene- 3-carboxamide32 A3

3-(3-methylphenyl)- 1-(4-phenylbutyl)urea 31 A12

2-{[(2- {bicyclo[4.1.0]heptane- 7-amido}pyridin-4-yl)methyl]sulfanyl}ethyl bicyclo[4.1.0]heptane- 7-carboxylate 30 1-F6

2-[2-({5-[1- (dimethylamino)ethyl]- 4-(4-fluorophenyl)-4H-1,2,4-triazol-3- yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta[b]thiophene- 3-carboxamide 29 1-F10

2-[2-({4-[(furan-2- yl)methyl]-5-(pyridin- 3-yl)-4H-1,2,4- triazol-3-yl}sulfanyl)propana- mido]-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 29 C07

1-[1-(4- chlorophenyl)- 1H,2H,3H,4H,9H- pyrido[3.4-b]indol-2-yl]-2-{[(4- fluorophenyl)methyl] sulfanyl}ethan-1-one 29 1-H9

1-[2-(benzylsulfanyl)ethyl]- 3-cyclopentylurea 26 2-A1 (also B5 onscreen 2)

N-benzyl-2-[2-({4- methyl-5- [(phenylcarbamoyl) methyl]-4H-1,2,4-triazol-3- yl}sulfanyl)acetamido]- 4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide 26 B12

N-{[4- (dimethylamino)phenyl]- methyl}-2-({[(3-methyl-phenyl)carbamoyl]- methyl}sulfanyl)- N-(propan-2- yl)acetamide 24 D04

ethyl 4-methyl-2-(2- {5H-[1,2,4]triazino[5,6- b]indol-3-ylsulfanyl}butanamido)- 1,3-thiazole-5- carboxylate 23 1-D1

2-[2-({4-benzyl-5-[1- (dimethylamino)propyl]- 4H-1,2,4-triazol-3-yl}sulfanyl)acetamido]- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide23 1-H5

2-(2-{[4-(4- fluorophenyl)-5- (pyridin-4-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide23 B11

9-oxo-N-(2- {[(thiophen-3- yl)methyl]sulfanyl}- ethyl)bicyclo[3.3.1]-nonane-3-carboxamide 23 1-C6

2-[2-({5-[(1,1-dioxo- 1λ⁶-thiolan-3- yl)methyl]-4-methyl-4H-1,2,4-triazol-3- yl}sulfanyl)acetamido]- 4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide 22 1-F4

2-(2-{[4-(2- methoxyphenyl)-5- methyl-4H-1,2,4- triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide 21 1-F1

2-(2-{[5-(furan-2-yl)- 4-phenyl-4H-1,2,4- triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide21 1-E10

2-(2-{[1-(2,3- dimethylphenyl)-1H- imidazol-2- yl]sulfanyl}propana-mido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 20 1-G2

2-{2-[(diphenyl-4H- 1,2,4-triazol-3- yl)sulfanyl]acetamido}-4,5,6,7-tetrahydro-1- benzothiophene-3- carboxamide 20 1-B8

2-(2-{[5-(2- methylfuran-3-yl)-4- phenyl-4H-1,2,4- triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 19 1-C1

N-(3-cyano-4,5,6,7- tetrahydro-1- benzothiophen-2-yl)-2-[(5-cyclopropyl-4- phenyl-4H-1,2,4- triazol-3- yl)sulfanyl]acetamide18 1-D12

2-(2-{5H,6H,7H,8H,9H- [1,2,4]triazolo[4,3- a]azepin-3-ylsulfanyl}propan- amido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 18 1-B9

N-(4-chlorophenyl)- 2-{2-[(5-cyclopropyl- 4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide 17 1-E4

2-{2-[(5-cyclopropyl- 4-methyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- N-(4-methoxyphenyl)- 4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide 17 1-E2

2-(2-{[4-(2- methoxyphenyl)-4H- 1,2,4-triazol-3- yl]sulfanyl}acetamido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 17 1-D10

2-(2-{[5-(2- methylfuran-3-yl)-4- phenyl-4H-1,2,4- triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide16 C01

2-{[4-(4- methylphenyl)-5- (morpholin-4-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}-N-[1- (propan-2-yl)-1H- pyrazol-5-yl]propanamide 15 B05

N-(2-{[(2- cyanophenyl)methyl] sulfanyl}ethyl)-2- {methyl[1-(3-nitrophenyl)ethyl] amino}acetamide 15 1-H11

2-{2-[(4-benzyl-5- cyclopropyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide 14 1-G8

2-{2-[(4-phenyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propana-mido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 14 A07

6-methyl-N-{[6-(4- methyl-1,4-diazepan-1- yl)pyridin-3-yl]methyl}-2,3-dihydro-1- benzothiophene-2- carboxamide 14 C02

5-methyl-2-{[1-(3- propyl-1,2,4-oxadiazol-5- yl)ethyl]sulfanyl}-1H-1,3-benzodiazole 13 1-C12

2-(2-{[4-cyclopropyl- 5-(thiophen-2-yl)- 4H-1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 13 1-F11

2-(2-{[4-phenyl-5- (pyridin-3-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide13 D02

7-(3,4-dimethylphenyl)-3- {[1-(3,4-dimethylphenyl)-1- oxopropan-2-yl]sulfanyl}-7H,8H- [1,2,4]triazolo[4,3- a]pyrazin-8-one 13 1-F3

2-(2-{[5-methyl-4-(4- methylphenyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide12 B2

2-[2-(phenylsulfanyl)ace- tamido]-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 12 1-C5

2-(2-{[4-(2- methylphenyl)-4H- 1,2,4-triazol-3- yl]sulfanyl}acetamido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 12 B08

N-(2,6-dimethylphenyl)-4- ({[3-(3-fluoro-4- methylphenyl)-1,2,4-oxadiazol-5- yl]methyl}sulfanyl)- butanamide 11 1-A1

2-(2-{[5-(4- chlorophenyl)-4- ethyl-4H-1,2,4- triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide11 E02

2-({[4-oxo-6- (propan-2-yl)- 3H,4H,4aH,7aH- thieno[2,3- d]pyrimidin-2-yl]methyl}sulfanyl)- N-[(pyridin-2- yl)methyl]acetamide 11 1-E3

2-{2-[(4-benzyl-5- cyclopropyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acetamido}- 6-methyl-4,5,6,7- tetrahydro-1-benzothiophene-3- carboxamide 10 1-E6

N-benzyl-2-{2-[(5- cyclopropyl-4-ethyl- 4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide 10 1-H3

2-{2-[(5-methyl-4- phenyl-4H-1,2,4- triazol-3- yl)sulfanyl]acetamido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 10 1-06

2-(2-{[5-(furan-2-yl)- 4-phenyl-4H-1,2,4- triazol-3-yl]sulfanyl}propana-mido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 10 1-B4

2-(2-{[4-methyl-5- (trifluoromethyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide10 C03

2-[(4- methoxyphenyl)sulfa- nyl]-N-(1H-pyrazol- 3-yl)propanamide 9 1-E7

2-(2-{[4-methyl-5-(2- methylphenyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide9 1-G6

2-[2-({4-cyclopropyl- 5-[(thiophen-2- yl)methyl]-4H-1,2,4- triazol-3-yl}sulfanyl)propana- mido]-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 9 B04

1-{bicyclo[2.2.1]heptan- 2-yl}-3-(2-{[(furan-2- yl)methyl]sulfanyl}ethyl)thiourea 9 D01

2-{[(7,8-dimethyl-4- oxo-1,4- dihydroquinolin-2-yl)methyl]sulfanyl}-N-(2- ethoxyphenyl)acetamide 8 1-H6

2-{2-[(5-benzyl-4- methyl-4H-1,2,4- triazol-3- yl)sulfanyl]propana-midoMH,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 7 1-G5

N-{3-cyano- 4H,5H,6H,7H,8H- cyclohepta[b]thiophen-2-yl}-2-[(5-cyclopropyl-4- phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]propana- mide 7 A5

3-(2-methylphenyl)- 1-(4-phenylbutyl)urea 6 pB

2-(4-phenylbutanamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide6 B10

N-(2,6-dimethylphenyl)-4- ({[5-(propan-2-yl)- 1,3-oxazol-2-yl]methyl}sulfanyl)- butanamide 6 1-H7

2-{2-[(5-benzyl-4- methyl-4H-1,2,4- triazol-3- yl)sulfanyl]acetamido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 6 1-A11

2-{2-[(5-cyclopropyl- 4-methyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 6-methyl-4,5,6,7- tetrahydro-1-benzothiophene-3- carboxamide 6 1-D11

2-{2-[(5-cyclopropyl- 4-ethyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 6-methyl-4,5,6,7- tetrahydro-1-benzothiophene-3- carboxamide 6 1-B10

1-cyclohexyl-3-(2- {[(2-fluorophenyl)methyl] sulfanyl}ethyl)urea 5 1-D9

2-(2-({5-[(1,1-dioxo- 1λ⁶-thiolan-3- yl)methyl]-4-methyl-4H-1,2,4-triazol-3- yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta[b]thiophene- 3-carboxamide 5 1-E8

2-(2-{[1-(3- fluorophenyl)-1H- imidazol-2- yl]sulfanyl}propanamido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide 4 1-G3

2-(2-{[4-phenyl-5- (pyridin-3-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide 4 2-A2

2-{2-[(dicyclopropyl- 4H-1,2,4-triazol-3- yl)sulfanyl]acetamido}-4,5,6,7-tetrahydro-1- benzothiophene-3- carboxamide 4 B4

2-{2-[(4-benzyl-5- cyclopropyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propana-mido}thiophene-3- carboxamide 4 D05

5-methoxy-3′-(2- methylbenzoyl)-1- {[3-(trifluoromethyl)-phenyl]methyl}-1,2- dihydrospiro[indole- 3,2′-[1,3]thiazolidine]-2- one4 A11

1-(4-methylphenyl)- 5-({1-[3-(4H-1,2,4- triazol-3-yl)-1,2,4-oxadiazol-5- yl]ethyl}sulfanyl)-1H- 1,2,3,4-tetrazole 4 E07

5-[2-(benzylsulfanyl)ethyl]- 3-(oxolan-3-yl)- 1,2,4-oxadiazole 3 1-G7

2-{2-[(1-benzyl-1H- imidazol-2- yl)sulfanyl]propana- mido}-4H,5H,6H-cyclopenta[b]thiophene- 3-carboxamide 3 2-A4

2-(2-{[4-ethyl-5-(2- phenylethyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 6-methyl-4,5,6,7- tetrahydro-1-benzothiophene-3- carboxamide 2 2-A5

2-{2-[(dimethyl-4H- 1,2,4-triazol-3- yl)sulfanyl]acetamido}- 4H,5H,6H-cyclopenta[b]thiophene- 3-carboxamide 2 1-A4

6-methyl-2-(2- {5H,6H,7H,8H,9H- [1,2,4]triazolo[4,3-a]azepin-3-ylsulfanyl}acetamido)- 4,5,6,7-tetrahydro- 1-benzothiophene-3-carboxamide 2 1-F8

2-(2-{[4-cyclopropyl- 5-(1H-indol-3-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide 2 1-D5

2-{2-[(5-cyclopropyl- 4-phenyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 6-methyl-4,5,6,7- tetrahydro-1-benzothiophene-3- carboxamide 1 1-D3

2-(2-{[5-methyl-4-(4- methylphenyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide 1 E05

N-[2-(benzyl- sulfanyl)ethyl]oxane-2- carboxamide 1 E04

N-(butan-2-yl)-2-{2- [(4-methyl- phenyl)sulfanyl]pro- panamido}benzamide1 1-C11

2-[2-({4-methyl-5- [(thiophen-2- yl)methyl]-4H-1,2,4- triazol-3-yl}sulfanyl)acelamido]- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide0 1-H2

2-(2-{[5-(4- chlorophenyl)-4- methyl-4H-1,2,4- triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide0 1-E9

2-[2-({5-[(1,1-dioxo- 1λ⁶-thiolan-3- yl)methyl]-4-methyl-4H-1,2,4-triazol-3- yl}sulfanyl)propana- mido]-4H,5H,6H-cyclopenta[b]thiophene- 3-carboxamide 0 C10

3-(2,5-dioxo-3-{[(E)- N-[(1- phenylethyl)imino]car- bamimidoyl]sul-fanyl}pyrrolidin-1- yl)benzoic acid −1 C04

2-{[2-(butan-2-yl)-3- oxo-2H,3H-imidazo[1,2- c]quinazolin-5-yl]sulfanyl}-N-(3,5- dimethoxyphenyl)pro- panamide −1 D8

2-[2-({5-[(4- methoxyphenoxy)- methyl]-4-methyl-4H- 1,2,4-triazol-3-yl}sulfanyl)propana- mido]-4H,5H,6H- cyclopenta[b)thiophene-3-carboxamide −1 B12

2-(2-{[4-(2- methoxyethyl)-5- (pyridin-4-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide −2 A05

2-[(4- bromophenyl)sulfanyl]- N-(2,3-dihydro- 1,4-benzodioxin-6-yl)propanamide −3 B3

2-(3-phenylpropanamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide−3 1-H1

2-(2-{[4-(2- methylphenyl)-5- (pyridin-4-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide−3 1-G10

2-(2-{5H,6H,7H,8H,9H- f1,2,4]triazolo[4,3- a]azepin-3-ylsulfanyl}acetamido)- 4,5,6,7-tetrahydro- 1-benzothiophene-3-carboxamide −3 1-C9

2-(2-{[4-methyl-5-(2- methylfuran-3-yl)- 4H-1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide −3 E06

5-methyl-N-{3-[(5- methyl-1,3,4-thiadiazol-2- yl)sulfanyl]propyl}-1H,4H,5H,6H,7H- pyrazolo[4,3-c]pyridine-3- carboxamide −3 1-E12

2-(2-{[4-(2- methylphenyl)-5- (pyridin-3-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide −3 1-E5

2-{2-[(5-cyclopropyl- 4-phenyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide −4 A2

3-(4-fluorophenyl)-1- (4-phenylbulyl)urea −4 D12

(1S,5R)-3-(6- methylpyridazin-3- yl)-6-[(pyridin-2- yl)methyl)-3,6-diazabicyclo[3.2.2] nonan-7-one −4 C11

N-(2,4- dimethylphenyl)-2- (2-{[(6-hydroxy-2,4- dioxo-1,2,3,4-tetrahydropyrimidin- 5-yl)[4-(propan-2- yl)phenyl]methyl]am-ino}-4-oxo-4,5- dihydro-1,3-thiazol- 5-yl)acetamide −4 1-H8

2-{2-[(diphenyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propana-mido}-4H,5H,6H- cyclopenta[b)thiophene- 3-carboxamide −5 C09

2-[({3-[5-methyl-2- (propan-2- yl)phenoxy]propyl}- sulfanyl)methyl]-1H-1,3-benzodiazole −6 1-A5

2-{2-[(5-cyclopropyl- 1-phenyl-1H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide−6 D07

N-(2-{[(3- chlorophenyl)methyl]- sulfanyl}ethyl)- 5H,6H,7H,8H,9H-[1,2,3,4]tetrazolo[1,5- a]azepine-9-carboxamide −7 1-F5

2-{2-[(5-cyclopropyl- 4-ethyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide −7 D10

4-[(4- methylphenyl)sulfanyl]- 1-({4H,5H,6H,7H-pyrazolo[1,5-a]pyrazin-2- yl}methyl)piperidine −8 C06

N-(3,4- dichlorophenyl)-2-{[2- (pyridin-2-yl)ethyl]sulfanyl}- acetamide−8 D11

1-cyclobutanecarbonyl- N-(2-{[(4-methyl- 1H-imidazol-5-yl)methyl]sulfanyl}- ethyl)piperidine-4- carboxamide −8 1-A12

2-(2-{[4-phenyl-5- (piperidin-1-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide −9 1-C3

6-methyl-2-{2-[(4- phenyl-4H-1,2,4- triazol-3- yl)sulfanyl]acetamido}-4,5,6,7-tetrahydro-1- benzothiophene-3- carboxamide −9 1-C7

2-{2-[(4-benzyl-5- cyclopropyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propana-mido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide −10 1-F2

2-(2-{[5-phenyl-4- (prop-2-en-1-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide−10 1-A3

2-(2-{[5-(4- fluorophenyl)-4- methyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide−10 E03

2-methyl-6-(2-{[(4- methyl-1H-imidazol-5- yl)methyl]sulfanyl}-ethyl)-2H,6H,7H- pyrazolo[4,3- d]pyrimidin-7-one −11 1-B2

N-(3-cyano-6- methyl-4,5,6,7- tetrahydro-1- benzothiophen-2-yl)-2-[(5-cyclopropyl-4- phenyl-4H-1,2,4- triazol-3- yl)sulfanyl]acetamide−12 1-B11

2-{2-[(5-cyclopropyl- 1-phenyl-1H-1,2,4- triazol-3-yl)sulfanyl]acetamido}- 6-methyl-4,5,6,7- tetrahydro-1-benzothiophene-3- carboxamide −13 1-C4

2-{2-[(4-phenyl-4H- 1,2,4-triazol-3- yl)sulfanyl]acetamido}- 4H,5H,6H-cyclopenta[b]thiophene- 3-carboxamide −14 A01

N-(2H-1,3- benzodioxol-5-yl)-2- {[4-benzyl-5- (morpholin-4-yl)-4H-1,2,4-triazol-3- yl]sulfanyl)propana- mide −17 D03

2-{[2-oxo-2-(1,2,3,4- tetrahydroquinolin-1- yl)ethyl]sulfanyl}-N-phenylacetamide −18 1-C2

2-{2-[(4-benzyl-5- methyl-4H-1,2,4-triazol-3- yl)sulfanyl]acetamido}-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide −23 1-A2

2-(2-{[4-cyclopropyl- 5-(2-fluorophenyl)- 4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide−24 1-A7

2-(2-{[1-(4- methoxyphenyl)-1H- imidazol-2- yl]sulfanyl}propana-mido)-4H,5H,6H- cyclopenta[b]thiophene- 3-carboxamide −26 1-F7

2-(2-{[4-phenyl-5- (thiophen-2-yl)-4H- 1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide −31 1-A6

2-(2-{[4-ethyl-5-(2- methylfuran-3-yl)- 4H-1,2,4-triazol-3-yl]sulfanyl}propana- mido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide −31 1-B5

N-benzyl-2-{2-[(5- cyclopropyl-4- methyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide

In some embodiments, the mitofusin modulating agent can comprise amethylated cyclohexy, a backbone, and a substituted triazole ring (seee.g., FIG. 46).

In some embodiments, the mitofusin modulating agent can comprise one ofthe following compounds:

(see e.g., FIG. 48).

The term “imine” or “imino”, as used herein, unless otherwise indicated,includes a functional group or chemical compound containing acarbon-nitrogen double bond. The expression “imino compound”, as usedherein, unless otherwise indicated, refers to a compound that includesan “imine” or an “imino” group as defined herein. The “imine” or “imino”group can be optionally substituted.

The term “hydroxyl”, as used herein, unless otherwise indicated,includes —OH. The “hydroxyl” can be optionally substituted.

The terms “halogen” and “halo”, as used herein, unless otherwiseindicated, include a chlorine, chloro, Cl; fluorine, fluoro, F; bromine,bromo, Br; or iodine, iodo, or I.

The term “acetamide”, as used herein, is an organic compound with theformula CH₃CONH₂. The “acetamide” can be optionally substituted.

The term “aryl”, as used herein, unless otherwise indicated, include acarbocyclic aromatic group. Examples of aryl groups include, but are notlimited to, phenyl, benzyl, naphthyl, or anthracenyl. The “aryl” can beoptionally substituted.

The terms “amine” and “amino”, as used herein, unless otherwiseindicated, include a functional group that contains a nitrogen atom witha lone pair of electrons and wherein one or more hydrogen atoms havebeen replaced by a substituent such as, but not limited to, an alkylgroup or an aryl group. The “amine” or “amino” group can be optionallysubstituted.

The term “alkyl”, as used herein, unless otherwise indicated, includessaturated monovalent hydrocarbon radicals having straight or branchedmoieties, such as but not limited to, methyl, ethyl, propyl, butyl,pentyl, hexyl, octyl groups, etc. Representative straight-chain loweralkyl groups include, but are not limited to, -methyl, -ethyl,-n-propyl, -n-butyl, -n-pentyl, -n-hexyl, -n-heptyl and -n-octyl; whilebranched lower alkyl groups include, but are not limited to, -isopropyl,-sec-butyl, -isobutyl, -tert-butyl, -isopentyl, 2-methylbutyl,2-methylpentyl, 3-methylpentyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl,2,2-dimethylpentyl, 2,3-dimethylpentyl, 3,3-dimethylpentyl,2,3,4-trimethylpentyl, 3-methylhexyl, 2,2-dimethylhexyl,2,4-dimethylhexyl, 2,5-dimethylhexyl, 3,5-dimethylhexyl,2,4-dimethylpentyl, 2-methylheptyl, 3-methylheptyl, unsaturated C₁₋₈alkyls include, but are not limited to, -vinyl, -allyl, -1-butenyl,-2-butenyl, -isobutylenyl, -1-pentenyl, -2-pentenyl,-3-methyl-1-butenyl, -2-methyl-2-butenyl, -2,3-dimethyl-2-butenyl,1-hexyl, 2-hexyl, 3-hexyl, -acetylenyl, -propynyl, -1-butynyl,-2-butynyl, -1-pentynyl, -2-pentynyl, or -3-methyl-1 butynyl. An alkylcan be saturated, partially saturated, or unsaturated. The “alkyl” canbe optionally substituted.

The term “carboxyl”, as used herein, unless otherwise indicated,includes a functional group consisting of a carbon atom double bonded toan oxygen atom and single bonded to a hydroxyl group (—COOH). The“carboxyl” can be optionally substituted.

The term “alkenyl”, as used herein, unless otherwise indicated, includesalkyl moieties having at least one carbon-carbon double bond whereinalkyl is as defined above and including E and Z isomers of said alkenylmoiety. An alkenyl can be partially saturated or unsaturated. The“alkenyl” can be optionally substituted.

The term “alkynyl”, as used herein, unless otherwise indicated, includesalkyl moieties having at least one carbon-carbon triple bond whereinalkyl is as defined above. An alkynyl can be partially saturated orunsaturated. The “alkynyl” can be optionally substituted.

The term “acyl”, as used herein, unless otherwise indicated, includes afunctional group derived from an aliphatic carboxylic acid, by removalof the hydroxyl (—OH) group. The “acyl” can be optionally substituted.

The term “alkoxyl”, as used herein, unless otherwise indicated, includesO-alkyl groups wherein alkyl is as defined above and O representsoxygen. Representative alkoxyl groups include, but are not limited to,—O-methyl, —O-ethyl, —O-n-propyl, —O-n-butyl, —O-n-pentyl, —O-n-hexyl,—O-n-heptyl, —O-n-octyl, —O-isopropyl, —O-sec-butyl, —O-isobutyl,—O-tert-butyl, —O-isopentyl, —O-2-methylbutyl, —O-2-methylpentyl,—O-3-methylpentyl, —O-2,2-dimethylbutyl, —O-2,3-dimethylbutyl,—O-2,2-dimethylpentyl, —O-2,3-dimethylpentyl, —O-3,3-dimethylpentyl,—O-2,3,4-trimethylpentyl, —O-3-methylhexyl, —O-2,2-dimethylhexyl,—O-2,4-dimethylhexyl, —O-2,5-dimethylhexyl, —O-3,5-dimethylhexyl,—O-2,4dimethylpentyl, —O-2-methylheptyl, —O-3-methylheptyl, —O-vinyl,—O-allyl, —O-1-butenyl, —O-2-butenyl, —O-isobutylenyl, —O-1-pentenyl,—O-2-pentenyl, —O-3-methyl-1-butenyl, —O-2-methyl-2-butenyl,—O-2,3-dimethyl-2-butenyl, —O-1-hexyl, —O-2-hexyl, —O-3-hexyl,—O-acetylenyl, —O-propynyl, —O-1-butynyl, —O-2-butynyl, —O-1-pentynyl,—O-2-pentynyl, —O-3-methyl-1-butynyl, —O— cyclopropyl, —O-cyclobutyl,—O-cyclopentyl, —O-cyclohexyl, —O-cycloheptyl, —O— cyclooctyl,—O-cyclononyl, —O-cyclodecyl, —O—CH₂-cyclopropyl, —O—CH₂-cyclobutyl,—O—CH₂-cyclopentyl, —O—CH₂-cyclohexyl, —O—CH₂-cycloheptyl,—O—CH₂-cyclooctyl, —O—CH₂-cyclononyl, —O—CH₂-cyclodecyl,—O—(CH₂)_(n)-cyclopropyl, —O—(CH₂)_(n)-cyclobutyl,—O—(CH₂)_(n)-cyclopentyl, —O—(CH₂)_(n)-cyclohexyl,—O—(CH₂)_(n)-cycloheptyl, —O—(CH₂)_(n)-cyclooctyl,—O—(CH₂)_(n)-cyclononyl, or —O—(CH₂)_(n)-cyclodecyl. An alkoxyl can besaturated, partially saturated, or unsaturated. The “alkoxyl” can beoptionally substituted. n can be between 1 and 20.

The term “cycloalkyl”, as used herein, unless otherwise indicated,includes a non-aromatic, saturated, partially saturated, or unsaturated,monocyclic or fused, spiro or unfused bicyclic or tricyclic hydrocarbonreferred to herein containing a total of from 3 to 10 carbon atoms.Examples of cycloalkyls include, but are not limited to, C₃₋₁₀cycloalkyl groups include, but are not limited to, -cyclopropyl,-cyclobutyl, -cyclopentyl, -cyclopentadienyl, -cyclohexyl,-cyclohexenyl, -1,3-cyclohexadienyl, -1,4-cyclohexadienyl, -cycloheptyl,-1,3-cycloheptadienyl, -1,3,5-cycloheptatrienyl, -cyclooctyl, and-cyclooctadienyl. The term “cycloalkyl” also includes -loweralkyl-cycloalkyl, wherein lower alkyl and cycloalkyl are as definedherein. Examples of -lower alkyl-cycloalkyl groups include, but are notlimited to, —CH₂-cyclopropyl, —CH₂-cyclobutyl, —CH₂-cyclopentyl,—CH₂-cyclopentadienyl, —CH₂— cyclohexyl, —CH₂-cycloheptyl, or—CH₂-cyclooctyl. The “cycloalkyl” can be optionally substituted.

The term “heterocyclyl” (e.g., a “heteroaryl”), as used herein, unlessotherwise indicated, includes an aromatic or non-aromatic cycloalkyl inwhich one to four of the ring carbon atoms are independently replacedwith a heteroatom from the group consisting of O, S and N.Representative examples of a heterocycle include, but are not limitedto, benzofuranyl, benzothiophene, indolyl, benzopyrazolyl, coumarinyl,isoquinolinyl, pyrrolyl, pyrrolidinyl, thiophenyl, furanyl, thiazolyl,imidazolyl, pyrazolyl, triazolyl, quinolinyl, pyrimidinyl, pyridinyl,pyridonyl, pyrazinyl, pyridazinyl, isothiazolyl, isoxazolyl,(1,4)-dioxane, (1,3)-dioxolane, 4,5-dihydro-1H-imidazolyl, ortetrazolyl. Heterocycles can be substituted or unsubstituted.Heterocycles can also be bonded at any ring atom (i.e., at any carbonatom or heteroatom of the heterocyclic ring). A heterocyclic can besaturated, partially saturated, or unsaturated. The “heterocyclic” canbe optionally substituted.

The term “indole”, as used herein, is an aromatic heterocyclic organiccompound with formula C₈H₇N. It has a bicyclic structure, consisting ofa six-membered benzene ring fused to a five-membered nitrogen-containingpyrrole ring. The “indole” can be optionally substituted.

The term “cyano”, as used herein, unless otherwise indicated, includes a—CN group. The “cyano” can be optionally substituted.

The term “alcohol”, as used herein, unless otherwise indicated, includesa compound in which the hydroxyl functional group (—OH) is bound to acarbon atom. In particular, this carbon center should be saturated,having single bonds to three other atoms. The “alcohol” can beoptionally substituted.

The term “solvate” is intended to mean a solvate form of a specifiedcompound that retains the effectiveness of such compound. Examples ofsolvates include compounds of the invention in combination with, forexample: water, isopropanol, ethanol, methanol, dimethylsulfoxide(DMSO), ethyl acetate, acetic acid, or ethanolamine.

The term “mmol”, as used herein, is intended to mean millimole. The term“equiv”, as used herein, is intended to mean equivalent. The term “mL”,as used herein, is intended to mean milliliter. The term “g”, as usedherein, is intended to mean gram. The term “kg”, as used herein, isintended to mean kilogram. The term “μg”, as used herein, is intended tomean micrograms. The term “h”, as used herein, is intended to mean hour.The term “min”, as used herein, is intended to mean minute. The term“M”, as used herein, is intended to mean molar. The term “μL”, as usedherein, is intended to mean microliter. The term “μM”, as used herein,is intended to mean micromolar. The term “nM”, as used herein, isintended to mean nanomolar. The term “N”, as used herein, is intended tomean normal. The term “amu”, as used herein, is intended to mean atomicmass unit. The term “° C.”, as used herein, is intended to mean degreeCelsius. The term “wt/wt”, as used herein, is intended to meanweight/weight. The term “v/v”, as used herein, is intended to meanvolume/volume. The term “MS”, as used herein, is intended to mean massspectroscopy. The term “HPLC”, as used herein, is intended to mean highperformance liquid chromatograph. The term “RT”, as used herein, isintended to mean room temperature. The term “e.g.”, as used herein, isintended to mean example. The term “N/A”, as used herein, is intended tomean not tested.

As used herein, the expression “pharmaceutically acceptable salt” refersto pharmaceutically acceptable organic or inorganic salts of a compoundof the invention. Preferred salts include, but are not limited, tosulfate, citrate, acetate, oxalate, chloride, bromide, iodide, nitrate,bisulfate, phosphate, acid phosphate, isonicotinate, lactate,salicylate, acid citrate, tartrate, oleate, tannate, pantothenate,bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate,gluconate, glucaronate, saccharate, formate, benzoate, glutamate,methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate,or pamoate (i.e., 1,1′-methylene-bis-(2-hydroxy-3-naphthoate)) salts. Apharmaceutically acceptable salt may involve the inclusion of anothermolecule such as an acetate ion, a succinate ion or other counterion.The counterion may be any organic or inorganic moiety that stabilizesthe charge on the parent compound. Furthermore, a pharmaceuticallyacceptable salt may have more than one charged atom in its structure.Instances where multiple charged atoms are part of the pharmaceuticallyacceptable salt can have multiple counterions. Hence, a pharmaceuticallyacceptable salt can have one or more charged atoms and/or one or morecounterion. As used herein, the expression “pharmaceutically acceptablesolvate” refers to an association of one or more solvent molecules and acompound of the invention. Examples of solvents that formpharmaceutically acceptable solvates include, but are not limited to,water, isopropanol, ethanol, methanol, DMSO, ethyl acetate, acetic acid,and ethanolamine. As used herein, the expression “pharmaceuticallyacceptable hydrate” refers to a compound of the invention, or a saltthereof, that further includes a stoichiometric or non-stoichiometricamount of water bound by non-covalent intermolecular forces.

MFN1 or MFN2

Mitochondria generate ATP that fuels neuronal activity. Mitochondriamust fuse in order to exchange genomes and promote mutual repair. Theinitial stages of mitochondrial fusion proceed through thephysiochemical actions of two closely related dynamin family GTPases,mitofusins (Mfn) 1 and 2. The obligatory first step leading tomitochondrial fusion is molecular tethering of two mitochondria viahomo- or hetero-oligomerization (in trans) of extended Mfn1 or Mfn2carboxyl termini. Subsequently, GTP binding to and hydrolysis by Mfn1 orMfn2 promotes irreversible physical fusion of the organellar outermembranes.

Mitofusins (Mfn) belong to a class of highly conserved GTPases which arelocated on the outer membrane of mitochondria in mammals, flies, theworm and budding yeast. Each of Mfn1 and Mfn2, the mitofusins present inmammals, are anchored to the outer membrane by two transmembrane domainssuch that their N-terminus and C-terminus are exposed to the cytoplasm.Mitofusins on different organelles undergo transdimerization throughanti-parallel binding of their extended carboxy terminal α-helicaldomains to form mitochondria-mitochondria tethers—the obligate initialstep in mitochondrial fusion (Koshiba et al., 2004, Science,305:858-861). Conventional wisdom is that mitofusins existconstitutively in this “active” extended molecular conformation whichsupports mitochondrial tethering, although other possible conformationsand the likelihood of functionally relevant molecular plasticity havenot been rigorously tested. The components involved in mitochondrialtethering involve intermolecular and possibly intramolecularinteractions of particular Mfn1 and Mfn2 domains. These interactionswere further studied and exploited in the design and testing ofcompositions which affect the interactions and the resultantmitochondrial function.

Mfn1 and Mfn2 share a common domain structure. The amino terminal GTPasedomain is followed by a coiled-coiled heptad repeat region (HR1), twoadjacent small transmembrane domains, and a carboxyl terminal coiledheptad repeat region (HR2). Amino acid conservation between Mfn1 andMfn2 varies by domain, being most highly conserved in the GTPase,transmembrane, and HR2 domains. HR2 domains extending from Mfn1molecules located on different mitochondria can bind to each other,forming inter-molecular HR2-HR2 interactions that link the molecules andtether the organelles (Koshiba et al. ibid). HR2 can also bind to HR1(Huang et al., 2011, PLoS One, 6:e20655), although there has been nodetermination of whether this is an inter- or intra-molecularinteraction.

The crystal structure of bacterial dynamin-like protein (OLP) (Low andLowe, 2006, Nature, 444:766-769; Protein Data Bank (PDB) ID No. 2J69)was used to model Mfn2 structure. The domain sequences of the OLP andMfn2 proteins were aligned. The alignment and modeling of Mfn2 based onthe OLP structure provided a template for the expansion and refining ofthe identities of HR2 amino acids that mediate inter-molecular HR2-HR2tethering (Koshiba et al., 2004, Science, 305:858-861). This analysisled to the novel conception that these same amino acids mediateinter-molecular antiparallel binding of HR2 to HR2 (see e.g., FIG. 2A)and intra-molecular antiparallel binding of HR2 to HR1.

Mitochondria-Associated Diseases, Disorders, or Conditions

The present disclosure provides for compositions and methods oftreatment for treating mitochondria-related diseases, disorders, orconditions such as diseases or disorders associated with mitofusin 1(Mfn1) and/or mitofusin 2 (Mfn2) and mitochondrial dysfunction. Amitochondria-associated disease, disorder, or condition can be a diseaseassociated with mitochondrial dysfunction, fragmentation, or fusion orassociated with dysfunction in Mfn1 or Mfn2 unfolding. Mitochondriadysfunction can be caused by mutations.

Mitochondria transit within cells and undergo fusion to exchange genomesand promote mutual repair. Mitochondrial fusion and subcellulartrafficking are mediated in part by mitofusins (Mfn) 1 and 2. Geneticmutations in Mfn2 that suppress mitochondrial fusion and motility causeCharcot Marie Tooth Disease 2A (CMT2A), the most common heritable axonalneuropathy. Mitochondrial fragmentation, dysfunction, and dysmotilityare also central features of other genetic neurodegenerative syndromes,such as amyotrophic lateral sclerosis, Huntington's disease, Parkinson'sdisease, and Alzheimer's disease. Because no therapeutics exist thatdirectly enhance mitochondrial fusion or trafficking, these diseases areunrelenting and irreversible.

As described herein, mitochondria-related diseases, disorders, orconditions can be any disease disorder or condition that is related tomitochondrial dysfunction. Mitochondrial dysfunction is implicated inchronic degenerative neurological conditions such as Alzheimer's,Parkinson's, and Huntington's diseases. For example, the geneticneurodegenerative condition, Charcot Marie Tooth Disease (type 2A) (CMT)or Hereditary motor and sensory neuropathy, is caused by multipleloss-of-function mutations of Mfn2. The underlying mechanism that causesthis debilitating neuropathy is impaired mitochondrial fusion.Currently, because there are no pharmacological Mfn agonists, there isno treatment for CMT.

Mitochondria-associated diseases, disorders, or conditions can beAlzheimer's disease, Parkinson's disease, Huntington's disease, CharcotMarie Tooth Disease (type 2A) (CMT), hereditary motor and sensoryneuropathy, autism, autosomal dominant optic atrophy (ADOA), musculardystrophy, Lou Gehrig's disease, cancer, mitochondrial myopathy,Diabetes mellitus and deafness (DAD), Leber's hereditary opticneuropathy (LHON), Leigh syndrome, subacute sclerosing encephalopathy,Neuropathy, ataxia, retinitis pigmentosa, and ptosis (NARP),Myoneurogenic gastrointestinal encephalopathy (MNGIE), MyoclonicEpilepsy with Ragged Red Fibers (MERRF), Mitochondrial myopathy,encephalomyopathy, lactic acidosis, stroke-like symptoms (MELAS), mtDNAdepletion, mitochondrial neurogastrointestinal encephalomyopathy(MNGIE), Dysautonomic Mitochondrial Myopathy, MitochondrialChannelopathy, or pyruvate dehydrogenase complex deficiency (PDCD/PDH).

Symptoms that can be treated with the methods as described herein caninclude poor growth, loss of muscle coordination, muscle weakness,visual problems, hearing problems, learning disabilities, heart disease,liver disease, kidney disease, gastrointestinal disorders, respiratorydisorders, neurological problems, autonomic dysfunction, and dementia.

Neurodeqenerative Disease

As described herein, mitofusin agonists (e.g., chimera B-A/I) rapidlyreverse mitochondrial dysmotility in sciatic nerve axons of a mousemodel of Charcot Marie Tooth disease. Because impaired mitochondrialfusion, fitness, and/or trafficking also contribute to neuronaldegeneration in various neurodegenerative diseases (e.g., in CharcotMarie Tooth disease (CMT2A), Huntington's disease, Parkinson's disease,and Alzheimer's disease, and especially in Amyotrophic Lateral Sclerosis(ALS)), the present disclosure provides for compositions (e.g.,mitofusin agonists) and methods to treat such neurodegenerativediseases, disorders, or conditions.

For example, a neurodegenerative disease, disorder or condition can be adisease of impaired neuronal mitochondrial dynamism or trafficking, suchas a hereditary motor and sensory neuropathy (HMSN) (e.g., Charcot MarieTooth (CMT) disease), CMT1 (a dominantly inherited, hypertrophic,predominantly demyelinating form), CMT2 (a dominantly inheritedpredominantly axonal form), Dejerine-Sottas (severe form with onset ininfancy), CMTX (inherited in an X-linked manner), CMT4 (includes thevarious demyelinating autosomal recessive forms of Charcot-Marie-Toothdisease), hereditary sensory and autonomic neuropathy type IE,hereditary sensory and autonomic neuropathy type II, hereditary sensoryand autonomic neuropathy type V, HMSN types 1A and 1B (e.g., dominantlyinherited hypertrophic demyelinating neuropathies), HMSN type 2 (e.g.,dominantly inherited neuronal neuropathies), HMSN type 3 (e.g.,hypertrophic neuropathy of infancy [Dejerine-Sottas]), HMSN type 4(e.g., hypertrophic neuropathy [Refsum] associated with phytanic acidexcess), HMSN type 5 (associated with spastic paraplegia), or HMSN type6 (e.g., with optic atrophy).

As another example, a neurodegenerative disease, disorder or conditioncan be Alzheimer's disease, amyotrophic lateral sclerosis (ALS),Alexander disease, Alpers' disease, Alpers-Huttenlocher syndrome,alpha-methylacyl-CoA racemase deficiency, Andermann syndrome, Artssyndrome, ataxia neuropathy spectrum, ataxia (E.g., with oculomotorapraxia, autosomal dominant cerebellar ataxia, deafness, andnarcolepsy), autosomal recessive spastic ataxia of Charlevoix-Saguenay,Batten disease, beta-propeller protein-associated neurodegeneration,Cerebro-Oculo-Facio-Skeletal Syndrome (COFS), Corticobasal Degeneration,CLN1 disease, CLN10 disease, CLN2 disease, CLN3 disease, CLN4 disease,CLN6 disease, CLN7 disease, CLN8 disease, cognitive dysfunction,congenital insensitivity to pain with anhidrosis, dementia, familialencephalopathy with neuroserpin inclusion bodies, familial Britishdementia, familial Danish dementia, fatty acid hydroxylase-associatedneurodegeneration, Gerstmann-Straussler-Scheinker Disease,GM2-gangliosidosis (e.g., AB variant), HMSN type 7 (e.g., with retinitispigmentosa), Huntington's disease, infantile neuroaxonal dystrophy,infantile-onset ascending hereditary spastic paralysis, Huntington'sdisease (HD), infantile-onset spinocerebellar ataxia, juvenile primarylateral sclerosis, Kennedy's disease, Kuru, Leigh's Disease,Marinesco-Sjögren syndrome, Mild Cognitive Impairment (MCI),mitochondrial membrane protein-associated neurodegeneration, Motorneuron disease, Monomelic Amyotrophy, Motor neuron diseases (MND),Multiple System Atrophy, Multiple System Atrophy with OrthostaticHypotension (Shy-Drager Syndrome), multiple sclerosis, multiple systematrophy, neurodegeneration in Down's syndrome (NDS), neurodegenerationof aging, Neurodegeneration with brain iron accumulation, neuromyelitisoptica, pantothenate kinase-associated neurodegeneration, OpsoclonusMyoclonus, prion disease, Progressive Multifocal Leukoencephalopathy,Parkinson's disease (PD), PD-related disorders, polycysticlipomembranous osteodysplasia with sclerosing leukoencephalopathy, priondisease, progressive external ophthalmoplegia, riboflavin transporterdeficiency neuronopathy, Sandhoff disease, Spinal muscular atrophy(SMA), Spinocerebellar ataxia (SCA), Striatonigral degeneration,Transmissible Spongiform Encephalopathies (prion diseases), orWallerian-like degeneration.

Charcot Marie Tooth (CMT) Disease.

Charcot Marie Tooth (CMT) disease is an example of a non-curable andcurrently untreatable neurodegenerative disease, disorder, or condition,which can be characterized by mutations of Mfn2 and/or axonalneuropathy. As described herein, it was discovered that mitochondrialtransport, not the conventional wisdom that mitochondria size, isimplicated in CMT disease progression. It is shown here that the abilityof mitochondria to get from point A to point B is the cause ofprogression. CMT is a progressive disease, caused by mutation in Mfn2,and characterized by neuronal neuropathy. The disease affects the legsat 8 to 10 years of age, then upper limbs, muscle wasting, skeletaldeformities, and results in being wheelchair bound. The presentdisclosure provides for the discovery that the progression of CMT wasnot due to small mitochondria size but the length of mitochondrialtravel. As such, this disclosure provides for the evaluation ofmitochondrial trafficking as a route of therapy in the first mouse modelof disease. It was discovered that the mitochondria in the legs do notmove, but in the arm, there is mitochondria movement. As such, it wasdiscovered that Mfn2 pays a role in mitochondria trafficking. Datashowed that administration of a mitofusin modulating agent allowed forthe mitochondria to move in a mouse model where mitochondria were notpreviously moving, which is applicable in any neuropathy (e.g.,Huntington's disease, amyotrophic lateral sclerosis (ALS) or ALS-likesclerosis, Alzheimer's disease).

Neurological Disease

As described herein, mitofusin agonists (e.g., chimera B-A/I) rapidlyreverses mitochondrial dysmotility in sciatic nerve axons of a mousemodel of Charcot Marie Tooth disease. It is currently believed thatimpaired mitochondrial trafficking also contribute to neuronaldegeneration in various neurological diseases (e.g., in Huntington's,Parkinson's, and Alzheimer's diseases, and especially in AmyotrophicLateral Sclerosis (ALS)). As such, the present disclosure provides formethods and compositions to treat neurological diseases, disorders, orconditions. For example, a neurological disease, disorder, or conditioncan be Abulia; Agraphia; Alcoholism; Alexia; Alien hand syndrome;Allan-Herndon-Dudley syndrome; Alternating hemiplegia of childhood;Alzheimer's disease; Amaurosis fugax; Amnesia; Amyotrophic lateralsclerosis (ALS); Aneurysm; Angelman syndrome; Anosognosia; Aphasia;Apraxia; Arachnoiditis; Arnold-Chiari malformation; Asomatognosia;Asperger syndrome; Ataxia; Attention deficit hyperactivity disorder;ATR-16 syndrome; Auditory processing disorder; Autism spectrum; Behcetsdisease; Bipolar disorder; Bell's palsy; Brachial plexus injury; Braindamage; Brain injury; Brain tumor; Brody myopathy; Canavan disease;Capgras delusion; Carpal tunnel syndrome; Causalgia; Central painsyndrome; Central pontine myelinolysis; Centronuclear myopathy; Cephalicdisorder; Cerebral aneurysm; Cerebral arteriosclerosis; Cerebralatrophy; Cerebral autosomal dominant arteriopathy with subcorticalinfarcts and leukoencephalopathy (CADASIL); Cerebraldysgenesis-neuropathy-ichthyosis-keratoderma syndrome (CEDNIK syndrome);Cerebral gigantism; Cerebral palsy; Cerebral vasculitis; Cervical spinalstenosis; Charcot-Marie-Tooth disease; Chiari malformation; Chorea;Chronic fatigue syndrome; Chronic inflammatory demyelinatingpolyneuropathy (CIDP); Chronic pain; Cockayne syndrome; Coffin-Lowrysyndrome; Coma; Complex regional pain syndrome; Compression neuropathy;Congenital facial diplegia; Corticobasal degeneration; Cranialarteritis; Craniosynostosis; Creutzfeldt-Jakob disease; Cumulativetrauma disorders; Cushing's syndrome; Cyclothymic disorder; CyclicVomiting Syndrome (CVS); Cytomegalic inclusion body disease (CIBD);Cytomegalovirus Infection; Dandy-Walker syndrome; Dawson disease; DeMorsier's syndrome; Dejerine-Klumpke palsy; Dejerine-Sottas disease;Delayed sleep phase syndrome; Dementia; Dermatomyositis; Developmentalcoordination disorder; Diabetic neuropathy; Diffuse sclerosis; Diplopia;Disorders of consciousness; Down syndrome; Dravet syndrome; Duchennemuscular dystrophy; Dysarthria; Dysautonomia; Dyscalculia; Dysgraphia;Dyskinesia; Dyslexia; Dystonia; Empty sella syndrome; Encephalitis;Encephalocele; Encephalotrigeminal angiomatosis; Encopresis; Enuresis;Epilepsy; Epilepsy-intellectual disability in females; Erb's palsy;Erythromelalgia; Essential tremor; Exploding head syndrome; Fabry'sdisease; Fahr's syndrome; Fainting; Familial spastic paralysis; Febrileseizures; Fisher syndrome; Friedreich's ataxia; Fibromyalgia; Foville'ssyndrome; Fetal alcohol syndrome; Fragile X syndrome; FragileX-associated tremor/ataxia syndrome (FXTAS); Gaucher's disease;Generalized epilepsy with febrile seizures plus; Gerstmann's syndrome;Giant cell arteritis; Giant cell inclusion disease; Globoid CellLeukodystrophy; Gray matter heterotopia; Guillain-Barré syndrome;Generalized anxiety disorder; HTLV-1 associated myelopathy;Hallervorden-Spatz syndrome; Head injury; Headache; Hemifacial Spasm;Hereditary Spastic Paraplegia; Heredopathia atactica polyneuritiformis;Herpes zoster oticus; Herpes zoster; Hirayama syndrome; Hirschsprung'sdisease; Holmes-Adie syndrome; Holoprosencephaly; Huntington's disease;Hydranencephaly; Hydrocephalus; Hypercortisolism; Hypoxia;Immune-Mediated encephalomyelitis; Inclusion body myositis;Incontinentia pigmenti; Infantile Refsum disease; Infantile spasms;Inflammatory myopathy; Intracranial cyst; Intracranial hypertension;Isodicentric 15; Joubert syndrome; Karak syndrome; Kearns-Sayresyndrome; Kinsbourne syndrome; Kleine-Levin syndrome; Klippel Feilsyndrome; Krabbe disease; Kufor-Rakeb syndrome; Lafora disease;Lambert-Eaton myasthenic syndrome; Landau-Kleffner syndrome; Lateralmedullary (Wallenberg) syndrome; Learning disabilities; Leigh's disease;Lennox-Gastaut syndrome; Lesch-Nyhan syndrome; Leukodystrophy;Leukoencephalopathy with vanishing white matter; Lewy body dementia;Lissencephaly; Locked-in syndrome; Lou Gehrig's disease (amyotrophiclateral sclerosis (ALS)); Lumbar disc disease; Lumbar spinal stenosis;Lyme disease-Neurological Sequelae; Machado-Joseph disease(Spinocerebellar ataxia type 3); Macrencephaly; Macropsia; Mal dedebarquement; Megalencephalic leukoencephalopathy with subcorticalcysts; Megalencephaly; Melkersson-Rosenthal syndrome; Menieres disease;Meningitis; Menkes disease; Metachromatic leukodystrophy; Microcephaly;Micropsia; Migraine; Miller Fisher syndrome; Mini-stroke (transientischemic attack); Misophonia; Mitochondrial myopathy; Mobius syndrome;Monomelic amyotrophy; Morvan syndrome; Motor Neurone Disease—seeamyotrophic lateral sclerosis; Motor skills disorder; Moyamoya disease;Mucopolysaccharidoses; Multi-infarct dementia; Multifocal motorneuropathy; Multiple sclerosis; Multiple system atrophy; Musculardystrophy; Myalgic encephalomyelitis; Myasthenia gravis; Myelinoclasticdiffuse sclerosis; Myoclonic Encephalopathy of infants; Myoclonus;Myopathy; Myotubular myopathy; Myotonia congenita; Narcolepsy;Neuro-Behçet's disease; Neurofibromatosis; Neuroleptic malignantsyndrome; Neurological manifestations of AIDS; Neurological sequelae oflupus; Neuromyotonia; Neuronal ceroid lipofuscinosis; Neuronal migrationdisorders; Neuropathy; Neurosis; Niemann-Pick disease; Non-24-hoursleep-wake disorder; Nonverbal learning disorder; O'Sullivan-McLeodsyndrome; Occipital Neuralgia; Occult Spinal Dysraphism Sequence;Ohtahara syndrome; Olivopontocerebellar atrophy; Opsoclonus myoclonussyndrome; Optic neuritis; Orthostatic Hypotension; Otosclerosis; Overusesyndrome; Palinopsia; Paresthesia; Parkinson's disease; Paramyotoniacongenita; Paraneoplastic diseases; Paroxysmal attacks; Parry-Rombergsyndrome; PANDAS; Pelizaeus-Merzbacher disease; Periodic paralyses;Peripheral neuropathy; Pervasive developmental disorders; Phantomlimb/Phantom pain; Photic sneeze reflex; Phytanic acid storage disease;Pick's disease; Pinched nerve; Pituitary tumors; PMG; Polyneuropathy;Polio; Polymicrogyria; Polymyositis; Porencephaly; Post-polio syndrome;Postherpetic neuralgia (PHN); Postural hypotension; Prader-Willisyndrome; Primary lateral sclerosis; Prion diseases; Progressivehemifacial atrophy; Progressive multifocal leukoencephalopathy;Progressive supranuclear palsy; Prosopagnosia; Pseudotumor cerebri;Quadrantanopia; Quadriplegia; Rabies; Radiculopathy; Ramsay Huntsyndrome type I; Ramsay Hunt syndrome type II; Ramsay Hunt syndrome typeIII—see Ramsay-Hunt syndrome; Rasmussen encephalitis; Reflexneurovascular dystrophy; Refsum disease; REM sleep behavior disorder;Repetitive stress injury; Restless legs syndrome; Retrovirus-associatedmyelopathy; Rett syndrome; Reye's syndrome; Rhythmic Movement Disorder;Romberg syndrome; Saint Vitus dance; Sandhoff disease; Schilder'sdisease (two distinct conditions); Schizencephaly; Sensory processingdisorder; Septo-optic dysplasia; Shaken baby syndrome; Shingles;Shy-Drager syndrome; Sjögren's syndrome; Sleep apnea; Sleeping sickness;Snatiation; Sotos syndrome; Spasticity; Spina bifida; Spinal cordinjury; Spinal cord tumors; Spinal muscular atrophy; Spinal and bulbarmuscular atrophy; Spinocerebellar ataxia; Split-brain;Steele-Richardson-Olszewski syndrome; Stiff-person syndrome; Stroke;Sturge-Weber syndrome; Stuttering; Subacute sclerosing panencephalitis;Subcortical arteriosclerotic encephalopathy; Superficial siderosis;Sydenham's chorea; Syncope; Synesthesia; Syringomyelia; Tarsal tunnelsyndrome; Tardive dyskinesia; Tardive dysphrenia; Tarlov cyst; Tay-Sachsdisease; Temporal arteritis; Temporal lobe epilepsy; Tetanus; Tetheredspinal cord syndrome; Thomsen disease; Thoracic outlet syndrome; TicDouloureux; Todd's paralysis; Tourette syndrome; Toxic encephalopathy;Transient ischemic attack; Transmissible spongiform encephalopathies;Transverse myelitis; Traumatic brain injury; Tremor; Trichotillomania;Trigeminal neuralgia; Tropical spastic paraparesis; Trypanosomiasis;Tuberous sclerosis; 22q13 deletion syndrome; Unverricht-Lundborgdisease; Vestibular schwannoma (Acoustic neuroma); Von Hippel-Lindaudisease (VHL); Viliuisk Encephalomyelitis (VE); Wallenberg's syndrome;West syndrome; Whiplash; Williams syndrome; Wilson's disease; Y-LinkedHearing Impairment; or Zellweger syndrome.

Molecular Engineering

The following definitions and methods are provided to better define thepresent invention and to guide those of ordinary skill in the art in thepractice of the present invention. Unless otherwise noted, terms are tobe understood according to conventional usage by those of ordinary skillin the relevant art.

The terms “heterologous DNA sequence”, “exogenous DNA segment” or“heterologous nucleic acid,” as used herein, each refer to a sequencethat originates from a source foreign to the particular host cell or, iffrom the same source, is modified from its original form. Thus, aheterologous gene in a host cell includes a gene that is endogenous tothe particular host cell but has been modified through, for example, theuse of DNA shuffling. The terms also include non-naturally occurringmultiple copies of a naturally occurring DNA sequence. Thus, the termsrefer to a DNA segment that is foreign or heterologous to the cell, orhomologous to the cell but in a position within the host cell nucleicacid in which the element is not ordinarily found. Exogenous DNAsegments are expressed to yield exogenous polypeptides. A “homologous”DNA sequence is a DNA sequence that is naturally associated with a hostcell into which it is introduced.

Expression vector, expression construct, plasmid, or recombinant DNAconstruct is generally understood to refer to a nucleic acid that hasbeen generated via human intervention, including by recombinant means ordirect chemical synthesis, with a series of specified nucleic acidelements that permit transcription or translation of a particularnucleic acid in, for example, a host cell. The expression vector can bepart of a plasmid, virus, or nucleic acid fragment. Typically, theexpression vector can include a nucleic acid to be transcribed operablylinked to a promoter.

A “promoter” is generally understood as a nucleic acid control sequencethat directs transcription of a nucleic acid. An inducible promoter isgenerally understood as a promoter that mediates transcription of anoperably linked gene in response to a particular stimulus. A promotercan include necessary nucleic acid sequences near the start site oftranscription, such as, in the case of a polymerase II type promoter, aTATA element. A promoter can optionally include distal enhancer orrepressor elements, which can be located as much as several thousandbase pairs from the start site of transcription.

A “transcribable nucleic acid molecule” as used herein refers to anynucleic acid molecule capable of being transcribed into a RNA molecule.Methods are known for introducing constructs into a cell in such amanner that the transcribable nucleic acid molecule is transcribed intoa functional mRNA molecule that is translated and therefore expressed asa protein product. Constructs may also be constructed to be capable ofexpressing antisense RNA molecules, in order to inhibit translation of aspecific RNA molecule of interest. For the practice of the presentdisclosure, conventional compositions and methods for preparing andusing constructs and host cells are well known to one skilled in the art(see e.g., Sambrook and Russel (2006) Condensed Protocols from MolecularCloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press,ISBN-10: 0879697717; Ausubel et al. (2002) Short Protocols in MolecularBiology, 5th ed., Current Protocols, ISBN-10: 0471250929; Sambrook andRussel (2001) Molecular Cloning: A Laboratory Manual, 3d ed., ColdSpring Harbor Laboratory Press, ISBN-10: 0879695773; Elhai, J. and Wolk,C. P. 1988. Methods in Enzymology 167, 747-754).

The “transcription start site” or “initiation site” is the positionsurrounding the first nucleotide that is part of the transcribedsequence, which is also defined as position +1. With respect to thissite all other sequences of the gene and its controlling regions can benumbered. Downstream sequences (i.e., further protein encoding sequencesin the 3′ direction) can be denominated positive, while upstreamsequences (mostly of the controlling regions in the 5′ direction) aredenominated negative.

A nucleic acid sequence or amino acid sequence (e.g., DNA, RNA, agenetic sequence, polynucleotide, oligonucleotide, primer, protein,polypeptide, peptide) can have about 80%; about 81%; about 82%; about83%; about 84%; about 85%; about 86%; about 87%; about 88%; about 89%;about 90%; about 91%; about 92%; about 93%; about 94%; about 95%; about96%; about 97%; about 98%; or about 99% sequence identity to a referencesequence or a naturally occurring sequence or contain at least onesubstitution modification to the reference sequence or naturallyoccurring sequence. Recitation of each of these discrete values isunderstood to include ranges between each value.

A nucleic acid sequence or an amino acid sequence can be operably linkedto a heterologous promoter.

“Operably-linked” or “functionally linked” refers preferably to theassociation of nucleic acid sequences on a single nucleic acid fragmentso that the function of one is affected by the other. For example, aregulatory DNA sequence is said to be “operably linked to” or“associated with” a DNA sequence that codes for an RNA or a polypeptideif the two sequences are situated such that the regulatory DNA sequenceaffects expression of the coding DNA sequence (i.e., that the codingsequence or functional RNA is under the transcriptional control of thepromoter). Coding sequences can be operably-linked to regulatorysequences in sense or antisense orientation. The two nucleic acidmolecules may be part of a single contiguous nucleic acid molecule andmay be adjacent. For example, a promoter is operably linked to a gene ofinterest if the promoter regulates or mediates transcription of the geneof interest in a cell.

A “construct” is generally understood as any recombinant nucleic acidmolecule such as a plasmid, cosmid, virus, autonomously replicatingnucleic acid molecule, phage, or linear or circular single-stranded ordouble-stranded DNA or RNA nucleic acid molecule, derived from anysource, capable of genomic integration or autonomous replication,comprising a nucleic acid molecule where one or more nucleic acidmolecule has been operably linked.

A constructs of the present disclosure can contain a promoter operablylinked to a transcribable nucleic acid molecule operably linked to a 3′transcription termination nucleic acid molecule. In addition, constructscan include but are not limited to additional regulatory nucleic acidmolecules from, e.g., the 3′-untranslated region (3′ UTR). Constructscan include but are not limited to the 5′ untranslated regions (5′ UTR)of an mRNA nucleic acid molecule which can play an important role intranslation initiation and can also be a genetic component in anexpression construct. These additional upstream and downstreamregulatory nucleic acid molecules may be derived from a source that isnative or heterologous with respect to the other elements present on thepromoter construct.

The term “transformation” refers to the transfer of a nucleic acidfragment into the genome of a host cell, resulting in genetically stableinheritance. Host cells containing the transformed nucleic acidfragments are referred to as “transgenic” cells, and organismscomprising transgenic cells are referred to as “transgenic organisms”.

“Transformed,” “transgenic,” and “recombinant” refer to a host cell ororganism such as a bacterium, cyanobacterium, animal or a plant intowhich a heterologous nucleic acid molecule has been introduced. Thenucleic acid molecule can be stably integrated into the genome asgenerally known in the art and disclosed (Sambrook 1989; Innis 1995;Gelfand 1995; Innis & Gelfand 1999). Known methods of PCR include, butare not limited to, methods using paired primers, nested primers, singlespecific primers, degenerate primers, gene-specific primers,vector-specific primers, partially mismatched primers, and the like. Theterm “untransformed” refers to normal cells that have not been throughthe transformation process.

“Wild-type” refers to a virus or organism found in nature without anyknown mutation.

Design, generation, and testing of the variant nucleotides, and theirencoded polypeptides, having the above required percent identities andretaining a required activity of the expressed protein is within theskill of the art. For example, directed evolution and rapid isolation ofmutants can be according to methods described in references including,but not limited to, Link et al. (2007) Nature Reviews 5(9), 680-688;Sanger et al. (1991) Gene 97(1), 119-123; Ghadessy et al. (2001) ProcNatl Acad Sci USA 98(8) 4552-4557. Thus, one skilled in the art couldgenerate a large number of nucleotide and/or polypeptide variantshaving, for example, at least 95-99% identity to the reference sequencedescribed herein and screen such for desired phenotypes according tomethods routine in the art.

Nucleotide and/or amino acid sequence identity percent (%) is understoodas the percentage of nucleotide or amino acid residues that areidentical with nucleotide or amino acid residues in a candidate sequencein comparison to a reference sequence when the two sequences arealigned. To determine percent identity, sequences are aligned and ifnecessary, gaps are introduced to achieve the maximum percent sequenceidentity. Sequence alignment procedures to determine percent identityare well known to those of skill in the art. Often publicly availablecomputer software such as BLAST, BLAST2, ALIGN2 or Megalign (DNASTAR)software is used to align sequences. Those skilled in the art candetermine appropriate parameters for measuring alignment, including anyalgorithms needed to achieve maximal alignment over the full-length ofthe sequences being compared. When sequences are aligned, the percentsequence identity of a given sequence A to, with, or against a givensequence B (which can alternatively be phrased as a given sequence Athat has or comprises a certain percent sequence identity to, with, oragainst a given sequence B) can be calculated as: percent sequenceidentity=X/Y100, where X is the number of residues scored as identicalmatches by the sequence alignment program's or algorithm's alignment ofA and B and Y is the total number of residues in B. If the length ofsequence A is not equal to the length of sequence B, the percentsequence identity of A to B will not equal the percent sequence identityof B to A.

Generally, conservative substitutions can be made at any position solong as the required activity is retained. So-called conservativeexchanges can be carried out in which the amino acid which is replacedhas a similar property as the original amino acid, for example theexchange of Glu by Asp, Gin by Asn, Val by lie, Leu by lie, and Ser byThr. For example, amino acids with similar properties can be Aliphaticamino acids (e.g., Glycine, Alanine, Valine, Leucine, Isoleucine);Hydroxyl or sulfur/selenium-containing amino acids (e.g., Serine,Cysteine, Selenocysteine, Threonine, Methionine); Cyclic amino acids(e.g., Proline); Aromatic amino acids (e.g., Phenylalanine, Tyrosine,Tryptophan); Basic amino acids (e.g., Histidine, Lysine, Arginine); orAcidic and their Amide (e.g., Aspartate, Glutamate, Asparagine,Glutamine). Deletion is the replacement of an amino acid by a directbond. Positions for deletions include the termini of a polypeptide andlinkages between individual protein domains. Insertions areintroductions of amino acids into the polypeptide chain, a direct bondformally being replaced by one or more amino acids. Amino acid sequencecan be modulated with the help of art-known computer simulation programsthat can produce a polypeptide with, for example, improved activity oraltered regulation. On the basis of this artificially generatedpolypeptide sequences, a corresponding nucleic acid molecule coding forsuch a modulated polypeptide can be synthesized in-vitro using thespecific codon-usage of the desired host cell.

“Highly stringent hybridization conditions” are defined as hybridizationat 65° C. in a 6×SSC buffer (i.e., 0.9 M sodium chloride and 0.09 Msodium citrate). Given these conditions, a determination can be made asto whether a given set of sequences will hybridize by calculating themelting temperature (T_(m)) of a DNA duplex between the two sequences.If a particular duplex has a melting temperature lower than 65° C. inthe salt conditions of a 6×SSC, then the two sequences will nothybridize. On the other hand, if the melting temperature is above 65° C.in the same salt conditions, then the sequences will hybridize. Ingeneral, the melting temperature for any hybridized DNA:DNA sequence canbe determined using the following formula: T_(m)=81.5°C.+16.6(log₁₀[Na⁺])+0.41 (fraction G/C content)−0.63(%formamide)−(600/l). Furthermore, the T_(m) of a DNA:DNA hybrid isdecreased by 1-1.5° C. for every 1% decrease in nucleotide identity (seee.g., Sambrook and Russel, 2006).

Host cells can be transformed using a variety of standard techniquesknown to the art (see, e.g., Sambrook and Russel (2006) CondensedProtocols from Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratory Press, ISBN-10: 0879697717; Ausubel et al. (2002)Short Protocols in Molecular Biology, 5th ed., Current Protocols,ISBN-10: 0471250929; Sambrook and Russel (2001) Molecular Cloning: ALaboratory Manual, 3d ed., Cold Spring Harbor Laboratory Press, ISBN-10:0879695773; Elhai, J. and Wolk, C. P. 1988. Methods in Enzymology 167,747-754). Such techniques include, but are not limited to, viralinfection, calcium phosphate transfection, liposome-mediatedtransfection, microprojectile-mediated delivery, receptor-mediateduptake, cell fusion, electroporation, and the like. The transfectedcells can be selected and propagated to provide recombinant host cellsthat comprise the expression vector stably integrated in the host cellgenome.

Exemplary nucleic acids which may be introduced to a host cell include,for example, DNA sequences or genes from another species, or even genesor sequences which originate with or are present in the same species,but are incorporated into recipient cells by genetic engineeringmethods. The term “exogenous” is also intended to refer to genes thatare not normally present in the cell being transformed, or perhapssimply not present in the form, structure, etc., as found in thetransforming DNA segment or gene, or genes which are normally presentand that one desires to express in a manner that differs from thenatural expression pattern, e.g., to over-express. Thus, the term“exogenous” gene or DNA is intended to refer to any gene or DNA segmentthat is introduced into a recipient cell, regardless of whether asimilar gene may already be present in such a cell. The type of DNAincluded in the exogenous DNA can include DNA which is already presentin the cell, DNA from another individual of the same type of organism,DNA from a different organism, or a DNA generated externally, such as aDNA sequence containing an antisense message of a gene, or a DNAsequence encoding a synthetic or modified version of a gene.

Host strains developed according to the approaches described herein canbe evaluated by a number of means known in the art (see e.g., Studier(2005) Protein Expr Purif. 41(1), 207-234; Gellissen, ed. (2005)Production of Recombinant Proteins: Novel Microbial and EukaryoticExpression Systems, Wiley-VCH, ISBN-10: 3527310363; Baneyx (2004)Protein Expression Technologies, Taylor & Francis, ISBN-10: 0954523253).

Methods of down-regulation or silencing genes are known in the art. Forexample, expressed protein activity can be down-regulated or eliminatedusing antisense oligonucleotides, protein aptamers, nucleotide aptamers,and RNA interference (RNAi) (e.g., small interfering RNAs (siRNA), shorthairpin RNA (shRNA), and micro RNAs (miRNA) (see e.g., Fanning andSymonds (2006) Handb Exp Pharmacol. 173, 289-303G, describing hammerheadribozymes and small hairpin RNA; Helene, C., et al. (1992) Ann. N.Y.Acad. Sci. 660, 27-36; Maher (1992) Bioassays 14(12): 807-15, describingtargeting deoxyribonucleotide sequences; Lee et al. (2006) Curr OpinChem Biol. 10, 1-8, describing aptamers; Reynolds et al. (2004) NatureBiotechnology 22(3), 326-330, describing RNAi; Pushparaj and Melendez(2006) Clinical and Experimental Pharmacology and Physiology 33(5-6),504-510, describing RNAi; Dillon et al. (2005) Annual Review ofPhysiology 67, 147-173, describing RNAi; Dykxhoorn and Lieberman (2005)Annual Review of Medicine 56, 401-423, describing RNAi). RNAi moleculesare commercially available from a variety of sources (e.g., Ambion, TX;Sigma Aldrich, MO; Invitrogen). Several siRNA molecule design programsusing a variety of algorithms are known to the art (see e.g., Cenixalgorithm, Ambion; BLOCK-iT™ RNAi Designer, Invitrogen; siRNA WhiteheadInstitute Design Tools, Bioinofrmatics & Research Computing). Traitsinfluential in defining optimal siRNA sequences include G/C content atthe termini of the siRNAs, Tm of specific internal domains of the siRNA,siRNA length, position of the target sequence within the CDS (codingregion), and nucleotide content of the 3′ overhangs.

Formulation

The agents and compositions described herein can be formulated by anyconventional manner using one or more pharmaceutically acceptablecarriers or excipients as described in, for example, Remington'sPharmaceutical Sciences (A. R. Gennaro, Ed.), 21st edition, ISBN:0781746736 (2005), incorporated herein by reference in its entirety.Such formulations will contain a therapeutically effective amount of abiologically active agent described herein, which can be in purifiedform, together with a suitable amount of carrier so as to provide theform for proper administration to the subject.

The term “formulation” refers to preparing a drug in a form suitable foradministration to a subject, such as a human. Thus, a “formulation” caninclude pharmaceutically acceptable excipients, including diluents orcarriers.

The term “pharmaceutically acceptable” as used herein can describesubstances or components that do not cause unacceptable losses ofpharmacological activity or unacceptable adverse side effects. Examplesof pharmaceutically acceptable ingredients can be those havingmonographs in United States Pharmacopeia (USP 29) and National Formulary(NF 24), United States Pharmacopeial Convention, Inc, Rockville, Md.,2005 (“USP/NF”), or a more recent edition, and the components listed inthe continuously updated Inactive Ingredient Search online database ofthe FDA. Other useful components that are not described in the USP/NF,etc. may also be used.

The term “pharmaceutically acceptable excipient,” as used herein, caninclude any and all solvents, dispersion media, coatings, antibacterialand antifungal agents, isotonic, or absorption delaying agents. The useof such media and agents for pharmaceutical active substances is wellknown in the art (see generally Remington's Pharmaceutical Sciences (A.R. Gennaro, Ed.), 21st edition, ISBN: 0781746736 (2005)). Except insofaras any conventional media or agent is incompatible with an activeingredient, its use in the therapeutic compositions is contemplated.Supplementary active ingredients can also be incorporated into thecompositions.

A “stable” formulation or composition can refer to a composition havingsufficient stability to allow storage at a convenient temperature, suchas between about 0° C. and about 60° C., for a commercially reasonableperiod of time, such as at least about one day, at least about one week,at least about one month, at least about three months, at least aboutsix months, at least about one year, or at least about two years.

The formulation should suit the mode of administration. The agents ofuse with the current disclosure can be formulated by known methods foradministration to a subject using several routes which include, but arenot limited to, parenteral, pulmonary, oral, topical, intradermal,intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal,epidural, ophthalmic, buccal, and rectal. The individual agents may alsobe administered in combination with one or more additional agents ortogether with other biologically active or biologically inert agents.Such biologically active or inert agents may be in fluid or mechanicalcommunication with the agent(s) or attached to the agent(s) by ionic,covalent, Van der Waals, hydrophobic, hydrophilic or other physicalforces.

Controlled-release (or sustained-release) preparations may be formulatedto extend the activity of the agent(s) and reduce dosage frequency.Controlled-release preparations can also be used to affect the time ofonset of action or other characteristics, such as blood levels of theagent, and consequently affect the occurrence of side effects.Controlled-release preparations may be designed to initially release anamount of an agent(s) that produces the desired therapeutic effect, andgradually and continually release other amounts of the agent to maintainthe level of therapeutic effect over an extended period of time. Inorder to maintain a near-constant level of an agent in the body, theagent can be released from the dosage form at a rate that will replacethe amount of agent being metabolized or excreted from the body. Thecontrolled-release of an agent may be stimulated by various inducers,e.g., change in pH, change in temperature, enzymes, water, or otherphysiological conditions or molecules.

Agents or compositions described herein can also be used in combinationwith other therapeutic modalities, as described further below. Thus, inaddition to the therapies described herein, one may also provide to thesubject other therapies known to be efficacious for treatment of thedisease, disorder, or condition.

Therapeutic Methods

Also provided is a process of treating a mitochondria-associateddisease, disorder, or condition in a subject in need administration of atherapeutically effective amount of mitofusin modulating agent, so as toprevent or treat a mitochondria-associated disease, disorder, orcondition.

For example, the compositions and methods described herein can be usedas a primary therapy for Charcot Marie Tooth, or adjunctive therapy forHuntington's, Parkinson's, and Alzheimer's diseases or ALS to reverse orretard progression.

Methods described herein are generally performed on a subject in needthereof. A subject in need of the therapeutic methods described hereincan be a subject having, diagnosed with, suspected of having, or at riskfor developing a mitochondria-associated disease, disorder, orcondition. A determination of the need for treatment will typically beassessed by a history and physical exam consistent with the disease orcondition at issue. Diagnosis of the various conditions treatable by themethods described herein is within the skill of the art. The subject canbe an animal subject, including a mammal, such as horses, cows, dogs,cats, sheep, pigs, mice, rats, monkeys, hamsters, guinea pigs, andchickens, and humans. For example, the subject can be a human subject.

Generally, a safe and effective amount of a mitofusin modulating agentis, for example, that amount that would cause the desired therapeuticeffect in a subject while minimizing undesired side effects. In variousembodiments, an effective amount of a mitofusin modulating agentdescribed herein can substantially inhibit mitochondria-associateddisease, disorder, or condition, slow the progress ofmitochondria-associated disease, disorder, or condition, or limit thedevelopment of mitochondria-associated disease, disorder, or condition.For example, a desired therapeutic effect can be a delay in peripheralneuropathy (e.g., over the course of three years) compared to placeboassessed by slower increase in modified composite CMT neuropathy score.As another example, a desired therapeutic effect can be reversal orabsence of progression of peripheral neuropathy compared to placebo, asindicated by lower or stable modified composite CMT neuropathy score.

According to the methods described herein, administration can beparenteral, pulmonary, oral, topical, intradermal, intramuscular,intraperitoneal, intravenous, subcutaneous, intranasal, epidural,ophthalmic, buccal, or rectal administration.

When used in the treatments described herein, a therapeuticallyeffective amount of a mitofusin modulating agent can be employed in pureform or, where such forms exist, in pharmaceutically acceptable saltform and with or without a pharmaceutically acceptable excipient. Forexample, the compounds of the present disclosure can be administered, ata reasonable benefit/risk ratio applicable to any medical treatment, ina sufficient amount to treat, prevent, or slow the progression ofmitochondria-associated disease, disorder, or condition.

The amount of a composition described herein that can be combined with apharmaceutically acceptable carrier to produce a single dosage form willvary depending upon the host treated and the particular mode ofadministration. It will be appreciated by those skilled in the art thatthe unit content of agent contained in an individual dose of each dosageform need not in itself constitute a therapeutically effective amount,as the necessary therapeutically effective amount could be reached byadministration of a number of individual doses.

Toxicity and therapeutic efficacy of compositions described herein canbe determined by standard pharmaceutical procedures in cell cultures orexperimental animals for determining the LD₅₀ (the dose lethal to 50% ofthe population) and the ED₅₀, (the dose therapeutically effective in 50%of the population). The dose ratio between toxic and therapeutic effectsis the therapeutic index that can be expressed as the ratio LD₅₀/ED₅₀,where larger therapeutic indices are generally understood in the art tobe optimal.

The specific therapeutically effective dose level for any particularsubject will depend upon a variety of factors including the disorderbeing treated and the severity of the disorder; activity of the specificcompound employed; the specific composition employed; the age, bodyweight, general health, sex and diet of the subject; the time ofadministration; the route of administration; the rate of excretion ofthe composition employed; the duration of the treatment; drugs used incombination or coincidental with the specific compound employed; andlike factors well known in the medical arts (see e.g., Koda-Kimble etal. (2004) Applied Therapeutics: The Clinical Use of Drugs, LippincottWilliams & Wilkins, ISBN 0781748453; Winter (2003) Basic ClinicalPharmacokinetics, 4^(th) ed., Lippincott Williams & Wilkins, ISBN0781741475; Sharqel (2004) Applied Biopharmaceutics & Pharmacokinetics,McGraw-Hill/Appleton & Lange, ISBN 0071375503). For example, it is wellwithin the skill of the art to start doses of the composition at levelslower than those required to achieve the desired therapeutic effect andto gradually increase the dosage until the desired effect is achieved.If desired, the effective daily dose may be divided into multiple dosesfor purposes of administration. Consequently, single dose compositionsmay contain such amounts or submultiples thereof to make up the dailydose. It will be understood, however, that the total daily usage of thecompounds and compositions of the present disclosure will be decided byan attending physician within the scope of sound medical judgment.

Again, each of the states, diseases, disorders, and conditions,described herein, as well as others, can benefit from compositions andmethods described herein. Generally, treating a state, disease,disorder, or condition includes preventing or delaying the appearance ofclinical symptoms in a mammal that may be afflicted with or predisposedto the state, disease, disorder, or condition but does not yetexperience or display clinical or subclinical symptoms thereof. Treatingcan also include inhibiting the state, disease, disorder, or condition,e.g., arresting or reducing the development of the disease or at leastone clinical or subclinical symptom thereof. Furthermore, treating caninclude relieving the disease, e.g., causing regression of the state,disease, disorder, or condition or at least one of its clinical orsubclinical symptoms. A benefit to a subject to be treated can be eitherstatistically significant or at least perceptible to the subject or to aphysician.

Administration of a mitofusin modulating agent can occur as a singleevent or over a time course of treatment. For example, a mitofusinmodulating agent can be administered daily, weekly, bi-weekly, ormonthly. For treatment of acute conditions, the time course of treatmentwill usually be at least several days. Certain conditions could extendtreatment from several days to several weeks. For example, treatmentcould extend over one week, two weeks, or three weeks. For more chronicconditions, treatment could extend from several weeks to several monthsor even a year or more.

Treatment in accord with the methods described herein can be performedprior to, concurrent with, or after conventional treatment modalitiesfor treating, preventing, or slowing the progression ofmitochondria-associated disease, disorder, or condition.

A mitofusin modulating agent can be administered simultaneously orsequentially with another agent, such as an antibiotic, ananti-inflammatory, or another agent. For example, a mitofusin modulatingagent can be administered simultaneously with another agent, such as anantibiotic or an anti-inflammatory. Simultaneous administration canoccur through administration of separate compositions, each containingone or more of a mitofusin modulating agent, an antibiotic, ananti-inflammatory, or another agent. Simultaneous administration canoccur through administration of one composition containing two or moreof mitofusin modulating agent, an antibiotic, an anti-inflammatory, oranother agent. A mitofusin modulating agent can be administeredsequentially with an antibiotic, an anti-inflammatory, or another agent.For example, a mitofusin modulating agent can be administered before orafter administration of an antibiotic, an anti-inflammatory, or anotheragent.

Administration

Agents and compositions described herein can be administered accordingto methods described herein in a variety of means known to the art. Theagents and composition can be used therapeutically either as exogenousmaterials or as endogenous materials. Exogenous agents are thoseproduced or manufactured outside of the body and administered to thebody. Endogenous agents are those produced or manufactured inside thebody by some type of device (biologic or other) for delivery within orto other organs in the body.

As discussed above, administration can be parenteral, pulmonary, oral,topical, transdermal (e.g., a transdermal patch) intradermal,intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal,epidural, ophthalmic, buccal, or rectal administration.

Agents and compositions described herein can be administered in avariety of methods well known in the arts. Administration can include,for example, methods involving oral ingestion, direct injection (e.g.,systemic or stereotactic), implantation of cells engineered to secretethe factor of interest, drug-releasing biomaterials, polymer matrices,gels, permeable membranes, osmotic systems, multilayer coatings,microparticles, implantable matrix devices, mini-osmotic pumps,implantable pumps, injectable gels and hydrogels, liposomes, micelles(e.g., up to 30 μm), nanospheres (e.g., less than 1 μm), microspheres(e.g., 1-100 μm), reservoir devices, a combination of any of the above,or other suitable delivery vehicles to provide the desired releaseprofile in varying proportions. Other methods of controlled-releasedelivery of agents or compositions will be known to the skilled artisanand are within the scope of the present disclosure.

Delivery systems may include, for example, an infusion pump which may beused to administer the agent or composition in a manner similar to thatused for delivering insulin or chemotherapy to specific organs ortumors. Typically, using such a system, an agent or composition can beadministered in combination with a biodegradable, biocompatiblepolymeric implant that releases the agent over a controlled period oftime at a selected site. Examples of polymeric materials includepolyanhydrides, polyorthoesters, polyglycolic acid, polylactic acid,polyethylene vinyl acetate, and copolymers and combinations thereof. Inaddition, a controlled release system can be placed in proximity of atherapeutic target, thus requiring only a fraction of a systemic dosage.

Agents can be encapsulated and administered in a variety of carrierdelivery systems. Examples of carrier delivery systems includemicrospheres, hydrogels, polymeric implants, smart polymeric carriers,and liposomes (see generally, Uchegbu and Schatzlein, eds. (2006)Polymers in Drug Delivery, CRC, ISBN-10: 0849325331). Carrier-basedsystems for molecular or biomolecular agent delivery can: provide forintracellular delivery; tailor biomolecule/agent release rates; increasethe proportion of biomolecule that reaches its site of action; improvethe transport of the drug to its site of action; allow colocalizeddeposition with other agents or excipients; improve the stability of theagent in vivo; prolong the residence time of the agent at its site ofaction by reducing clearance; decrease the nonspecific delivery of theagent to nontarget tissues; decrease irritation caused by the agent;decrease toxicity due to high initial doses of the agent; alter theimmunogenicity of the agent; decrease dosage frequency, improve taste ofthe product; or improve shelf life of the product.

Screening

Also provided are methods for screening (see e.g., Example 2, Example3). As described herein, a FRET method for screening and evaluatingsmall molecular regulators of mitochondrial tethering and fusion isprovided. Also provided herein is a binding assay for screening andevaluating small molecular regulators of mitochondrial tethering andfusion.

The term “FRET” as used herein refers to fluorescence resonance energytransfer between molecules. In FRET methods, one fluorophore is able toact as an energy donor and the other of which is an energy acceptormolecule. These are sometimes known as a reporter molecule and aquencher molecule respectively. The donor molecule is excited with aspecific wavelength of light for which it will normally exhibit afluorescence emission wavelength. The acceptor molecule is also excitedat this wavelength such that it can accept the emission energy of thedonor molecule by a variety of distance-dependent energy transfermechanisms. Generally the acceptor molecule accepts the emission energyof the donor molecule when they are in close proximity (e.g., on thesame, or a neighboring molecule). See for example U.S. Pat. Nos.5,707,804, 5,728,528, 5,853,992, and 5,869,255 (for a description ofFRET dyes), T Mergny et al., (1994) Nucleic Acid Res. 22:920-928, andWolf et al., (1988) Proc. Natl. Acad. Sci. USA 85:8790-8794 (for generaldescriptions and methods for FRET), each of which is hereby incorporatedby reference in its entirety.

With the modulating compounds and peptides available which have beenshown to activate mitochondrial fusion, assays can be designed andperformed to screen candidate agents or molecules for specificcompositions which can activate mitochondrial fusion. For example,identification of small molecule activators provides an alternatemodulating composition which may be more efficient to synthesize anduse. Candidate agents encompass numerous chemical classes, typicallysynthetic, semi-synthetic, or naturally-occurring inorganic or organicmolecules. Candidate agents include those found in large libraries ofsynthetic or natural compounds. Alternatively, libraries of naturalcompounds in the form of bacterial, fungal, plant and animal extractsare available from commercial resources or are readily producible. Insome embodiments, small molecule activators of mitochondrial fusionidentified through these screening assays can become promisingtherapeutic agents for treating diseases or disorders associated withdefects in mitochondrial fusion.

One screening assay can use the HR1 peptide or variant which has beenshown to increase mitochondrial aspect ratio. In this assay, the Mfn2protein or a fragment of the Mfn2 protein which contains the HR2 domainis immobilized to a solid substrate such as nitrocellulose or to thewell surface of a high throughput screen plate or array substrate. Theimmobilized protein or fragment is then incubated with the HR1 peptideor variant in a solution conducive to protein-protein interactions. TheHR1 peptide is conjugated to a detectable label such as FITC or otherfluorescent dye, generating a signal in each well or array position.Detectable labels are well-known in the art and include isotope,colorimetric, fluorescent, photochromic and electrochemical labels. Acandidate agent is assessed for its ability to compete with the HR1peptide for binding to the solid phase-bound Mfn2 protein or HR2 domain.An agent which can compete with the HR1 peptide for binding to Mfn2protein or HR2 will reduce or eliminate the signal from the label. Acandidate agent able compete with the HR1 peptide is an agent which canactivate mitochondrial aspect ratio and/or mitochondrial fusion.

In some embodiments, a method for identifying an agent or compound ableto bind to the Mfn2 protein is provided. In these embodiments, thecompound competes with the HR1 peptide for binding to Mfn2 or to afragment of Mfn2 comprising the HR2 domain. A test compound isidentified as active it if decreases the binding of the peptide, i.e.,its effect on the extent of binding is above a threshold level. Morespecifically, if the decrease in binding of the labeled HR1 peptide tothe solid phase bound Mfn2 protein or HR2 domain is a several-folddifferent between the control and experimental samples, the compoundwould be considered as having binding activity. Typically, a 2-fold or4-fold threshold difference in binding between the test and controlsamples is sought. In some embodiments, this agent increases themitochondrial aspect ratio when incubated in a cell.

In some embodiments, an alternative assay is provided to identify acomposition able to activate intermolecular binding of the HR2 domainsof two Mfn proteins. In this assay, a first population of Mfn2 proteinsis labeled with an acceptor fluorophore on its HR2 arm and a secondpopulation of Mfn2 proteins is labeled with a donor fluorophore on itsHR2 arm. Use of fluorophore donors and complementary acceptor moleculesfor FRET analysis is well known (see, e.g., Jager et al., 2005, ProteinSci, 14:2059-2068; Jager et al, 2006, Protein Sci, 15:640-646).Accordingly, as described above, when an HR2 arm is liberated from theconfiguration in which it is interacting with the HR1 domain within thecore of the Mfn protein, the free HR2 arm is able to interact with thefree HR2 arm of a second Mfn2 to facilitate mitochondrial tethering andsubsequent fusion. It follows that provided herein is an assay to screena population of agents or compounds for those that facilitatemitochondrial tethering and subsequent fusion wherein the population ofcandidate compounds is added to an array, wherein each well or positionin the array contains a test reaction mix which comprises a firstpopulation of Mfn2 proteins labeled at or near the HR2 arm with a donorfluorophore and a second population of Mfn2 proteins labeled at or nearthe HR2 arm with a acceptor fluorophore. The fluorescence is measured ineach test reaction mix and compared with a negative control reaction mixcontaining no HR2-binding peptide and a positive control reaction mixwhich contains an HR2-binding peptide and no candidate compound. Afluorescence signal which is greater in a test reaction mix containing acandidate compound is identified the candidate compound as an activatorof mitochondrial fusion.

In a third screening assay, interaction between the HR1 and HR2 domainsof a single Mfn2 protein is assessed. For example, a single Mfn2 proteinis labeled with a single FRET donor and acceptor pair, wherein the donoris positioned at or near the HR1 domain and the acceptor is positionedat or near the HR2 domain, or vice versa. Incubation of a peptide whichinhibits mitochondrial fusion (decreases mitochondrial aspect ratio)(e.g., the 367-384Gly peptide or variant thereof) will cause the HR2 armto extend, removing the quenching action of the FRET pair, resulting influorescence signal. Accordingly, a library of candidate modulatingmolecules can be screened by mixing each with the Mfn2 protein labeledwith a FRET donor acceptor pair. Any candidate molecule which increasesfluorescence of the labeled Mfn2 protein by at least 50%, 60%, 70%compared to the labeled Mfn2 protein in the absence of a candidatemolecule will be identified as an activator of mitochondrial fusion.

The subject methods find use in the screening of a variety of differentcandidate molecules (e.g., potentially therapeutic candidate molecules).Candidate substances for screening according to the methods describedherein include, but are not limited to, fractions of tissues or cells,nucleic acids, polypeptides, siRNAs, antisense molecules, aptamers,ribozymes, triple helix compounds, antibodies, and small (e.g., lessthan about 2000 mw, or less than about 1000 mw, or less than about 800mw) organic molecules or inorganic molecules including but not limitedto salts or metals.

Candidate molecules encompass numerous chemical classes, for example,organic molecules, such as small organic compounds having a molecularweight of more than 50 and less than about 2,500 Daltons. Candidatemolecules can comprise functional groups necessary for structuralinteraction with proteins, particularly hydrogen bonding, and typicallyinclude at least an amine, carbonyl, hydroxyl or carboxyl group, andusually at least two of the functional chemical groups. The candidatemolecules can comprise cyclical carbon or heterocyclic structures and/oraromatic or polyaromatic structures substituted with one or more of theabove functional groups.

A candidate molecule can be a compound in a library database ofcompounds. One of skill in the art will be generally familiar with, forexample, numerous databases for commercially available compounds forscreening (see e.g., ZINC database, UCSF, with 2.7 million compoundsover 12 distinct subsets of molecules; Irwin and Shoichet (2005) J ChemInf Model 45, 177-182). One of skill in the art will also be familiarwith a variety of search engines to identify commercial sources ordesirable compounds and classes of compounds for further testing (seee.g., ZINC database; eMolecules.com; and electronic libraries ofcommercial compounds provided by vendors, for example: ChemBridge,Princeton BioMolecular, Ambinter SARL, Enamine, ASDI, Life Chemicalsetc.).

Candidate molecules for screening according to the methods describedherein include both lead-like compounds and drug-like compounds. Alead-like compound is generally understood to have a relatively smallerscaffold-like structure (e.g., molecular weight of about 150 to about350 kD) with relatively fewer features (e.g., less than about 3 hydrogendonors and/or less than about 6 hydrogen acceptors; hydrophobicitycharacter x log P of about −2 to about 4) (see e.g., Angewante (1999)Chemie Int. ed. Engl. 24, 3943-3948). In contrast, a drug-like compoundis generally understood to have a relatively larger scaffold (e.g.,molecular weight of about 150 to about 500 kD) with relatively morenumerous features (e.g., less than about 10 hydrogen acceptors and/orless than about 8 rotatable bonds; hydrophobicity character x log P ofless than about 5) (see e.g., Lipinski (2000) J. Pharm. Tox. Methods 44,235-249). Initial screening can be performed with lead-like compounds.

When designing a lead from spatial orientation data, it can be useful tounderstand that certain molecular structures are characterized as being“drug-like”. Such characterization can be based on a set of empiricallyrecognized qualities derived by comparing similarities across thebreadth of known drugs within the pharmacopoeia. While it is notrequired for drugs to meet all, or even any, of these characterizations,it is far more likely for a drug candidate to meet with clinicalsuccessful if it is drug-like.

Several of these “drug-like” characteristics have been summarized intothe four rules of Lipinski (generally known as the “rules of fives”because of the prevalence of the number 5 among them). While these rulesgenerally relate to oral absorption and are used to predictbioavailability of compound during lead optimization, they can serve aseffective guidelines for constructing a lead molecule during rationaldrug design efforts such as may be accomplished by using the methods ofthe present disclosure.

The four “rules of five” state that a candidate drug-like compoundshould have at least three of the following characteristics: (i) aweight less than 500 Daltons; (ii) a log of P less than 5; (iii) no morethan 5 hydrogen bond donors (expressed as the sum of OH and NH groups);and (iv) no more than 10 hydrogen bond acceptors (the sum of N and Oatoms). Also, drug-like molecules typically have a span (breadth) ofbetween about 8 Å to about 15 Å.

Fragment-based lead discovery (FBLD) also known as fragment-based drugdiscovery (FBDD) is a method that can be used for finding lead compoundsas part of the drug discovery process. It is based on identifying smallchemical fragments, which may bind only weakly to the biological target,and then growing them or combining them to produce a lead with a higheraffinity. FBLD can be compared with high-throughput screening (HTS). InHTS, libraries with up to millions of compounds, with molecular weightsof around 500 Da, are screened, and nanomolar binding affinities aresought. In contrast, in the early phase of FBLD, libraries with a fewthousand compounds with molecular weights of around 200 Da may bescreened, and millimolar affinities can be considered useful.

In analogy to the rule of five, it has been proposed that idealfragments could follow the ‘rule of three’ (molecular weight <300, ClogP<3, the number of hydrogen bond donors and acceptors each should be <3and the number of rotatable bonds should be <3). Since the fragmentshave relatively low affinity for their targets, they should have highwater solubility so that they can be screened at higher concentrations.

In fragment-based drug discovery, the low binding affinities of thefragments can pose significant challenges for screening. Manybiophysical techniques have been applied to address this issue. Inparticular, ligand-observe nuclear magnetic resonance (NMR) methods suchas water-ligand observed via gradient spectroscopy (waterLOGSY),saturation transfer difference spectroscopy (STD-NMR), 19F NMRspectroscopy and inter-ligand Overhauser effect (ILOE) spectroscopy,protein-observe NMR methods such as 1H-15N heteronuclear single quantumcoherence (HSQC) that utilizes isotopically-labelled proteins, surfaceplasmon resonance (SPR) and isothermal titration calorimetry (ITC) areroutinely-used for ligand screening and for the quantification offragment binding affinity to the target protein.

Once a fragment (or a combination of fragments) have been identified,protein X-ray crystallography can be used to obtain structural models ofthe protein-fragment(s) complexes. Such information can then be used toguide organic synthesis for high-affinity protein ligands and enzymeinhibitors.

Advantages of screening low molecular weight fragment based librariesover traditional higher molecular weight chemical libraries can include:

(i) More hydrophilic hits in which hydrogen bonding is more likely tocontribute to affinity (enthalpically driven binding). It is generallymuch easier to increase affinity by adding hydrophobic groups(entropically driven binding), starting with a hydrophilic ligandincreases the chances that the final optimized ligand will not be toohydrophobic (log P<5).

(ii) Higher ligand efficiency so that the final optimized ligand willmore likely be relatively low in molecular weight (MW<500).

(iii) Since two to three fragments in theory can be combined to form anoptimized ligand, screening a fragment library of N compounds isequivalent to screening N2-N3 compounds in a traditional library.

Fragments can be less likely to contain sterically blocking groups thatinterfere with an otherwise favorable ligand-protein interaction,increasing the combinatorial advantage of a fragment library evenfurther.

Kits

Also provided are kits. Such kits can include an agent or compositiondescribed herein and, in certain embodiments, instructions foradministration. Such kits can facilitate performance of the methodsdescribed herein. When supplied as a kit, the different components ofthe composition can be packaged in separate containers and admixedimmediately before use. Components include, but are not limited to Mfn1,Mfn2, antagonist target peptides, agonist target peptides, or mitofusinmodulating agents. Such packaging of the components separately can, ifdesired, be presented in a pack or dispenser device which may containone or more unit dosage forms containing the composition. The pack may,for example, comprise metal or plastic foil such as a blister pack. Suchpackaging of the components separately can also, in certain instances,permit long-term storage without losing activity of the components.

Kits may also include reagents in separate containers such as, forexample, sterile water or saline to be added to a lyophilized activecomponent packaged separately. For example, sealed glass ampules maycontain a lyophilized component and in a separate ampule, sterile water,sterile saline or sterile each of which has been packaged under aneutral non-reacting gas, such as nitrogen. Ampules may consist of anysuitable material, such as glass, organic polymers, such aspolycarbonate, polystyrene, ceramic, metal or any other materialtypically employed to hold reagents. Other examples of suitablecontainers include bottles that may be fabricated from similarsubstances as ampules, and envelopes that may consist of foil-linedinteriors, such as aluminum or an alloy. Other containers include testtubes, vials, flasks, bottles, syringes, and the like. Containers mayhave a sterile access port, such as a bottle having a stopper that canbe pierced by a hypodermic injection needle. Other containers may havetwo compartments that are separated by a readily removable membrane thatupon removal permits the components to mix. Removable membranes may beglass, plastic, rubber, and the like.

In certain embodiments, kits can be supplied with instructionalmaterials. Instructions may be printed on paper or other substrate,and/or may be supplied as an electronic-readable medium, such as afloppy disc, mini-CD-ROM, CD-ROM, DVD-ROM, Zip disc, videotape, audiotape, and the like. Detailed instructions may not be physicallyassociated with the kit; instead, a user may be directed to an Internetweb site specified by the manufacturer or distributor of the kit.

Compositions and methods described herein utilizing molecular biologyprotocols can be according to a variety of standard techniques known tothe art (see, e.g., Sambrook and Russel (2006) Condensed Protocols fromMolecular Cloning: A Laboratory Manual, Cold Spring Harbor LaboratoryPress, ISBN-10: 0879697717; Ausubel et al. (2002) Short Protocols inMolecular Biology, 5th ed., Current Protocols, ISBN-10: 0471250929;Sambrook and Russel (2001) Molecular Cloning: A Laboratory Manual, 3ded., Cold Spring Harbor Laboratory Press, ISBN-10: 0879695773; Elhai, J.and Wolk, C. P. 1988. Methods in Enzymology 167, 747-754; Studier (2005)Protein Expr Purif. 41(1), 207-234; Gellissen, ed. (2005) Production ofRecombinant Proteins: Novel Microbial and Eukaryotic Expression Systems,Wiley-VCH, ISBN-10: 3527310363; Baneyx (2004) Protein ExpressionTechnologies, Taylor & Francis, ISBN-10: 0954523253).

Definitions and methods described herein are provided to better definethe present disclosure and to guide those of ordinary skill in the artin the practice of the present disclosure. Unless otherwise noted, termsare to be understood according to conventional usage by those ofordinary skill in the relevant art.

In some embodiments, numbers expressing quantities of ingredients,properties such as molecular weight, reaction conditions, and so forth,used to describe and claim certain embodiments of the present disclosureare to be understood as being modified in some instances by the term“about.” In some embodiments, the term “about” is used to indicate thata value includes the standard deviation of the mean for the device ormethod being employed to determine the value. In some embodiments, thenumerical parameters set forth in the written description and attachedclaims are approximations that can vary depending upon the desiredproperties sought to be obtained by a particular embodiment. In someembodiments, the numerical parameters should be construed in light ofthe number of reported significant digits and by applying ordinaryrounding techniques. Notwithstanding that the numerical ranges andparameters setting forth the broad scope of some embodiments of thepresent disclosure are approximations, the numerical values set forth inthe specific examples are reported as precisely as practicable. Thenumerical values presented in some embodiments of the present disclosuremay contain certain errors necessarily resulting from the standarddeviation found in their respective testing measurements. The recitationof ranges of values herein is merely intended to serve as a shorthandmethod of referring individually to each separate value falling withinthe range. Unless otherwise indicated herein, each individual value isincorporated into the specification as if it were individually recitedherein.

In some embodiments, the terms “a” and “an” and “the” and similarreferences used in the context of describing a particular embodiment(especially in the context of certain of the following claims) can beconstrued to cover both the singular and the plural, unless specificallynoted otherwise. In some embodiments, the term “or” as used herein,including the claims, is used to mean “and/or” unless explicitlyindicated to refer to alternatives only or the alternatives are mutuallyexclusive.

The terms “comprise,” “have” and “include” are open-ended linking verbs.Any forms or tenses of one or more of these verbs, such as “comprises,”“comprising,” “has,” “having,” “includes” and “including,” are alsoopen-ended. For example, any method that “comprises,” “has” or“includes” one or more steps is not limited to possessing only those oneor more steps and can also cover other unlisted steps. Similarly, anycomposition or device that “comprises,” “has” or “includes” one or morefeatures is not limited to possessing only those one or more featuresand can cover other unlisted features.

All methods described herein can be performed in any suitable orderunless otherwise indicated herein or otherwise clearly contradicted bycontext. The use of any and all examples, or exemplary language (e.g.“such as”) provided with respect to certain embodiments herein isintended merely to better illuminate the present disclosure and does notpose a limitation on the scope of the present disclosure otherwiseclaimed. No language in the specification should be construed asindicating any non-claimed element essential to the practice of thepresent disclosure.

Groupings of alternative elements or embodiments of the presentdisclosure disclosed herein are not to be construed as limitations. Eachgroup member can be referred to and claimed individually or in anycombination with other members of the group or other elements foundherein. One or more members of a group can be included in, or deletedfrom, a group for reasons of convenience or patentability. When any suchinclusion or deletion occurs, the specification is herein deemed tocontain the group as modified thus fulfilling the written description ofall Markush groups used in the appended claims.

Citation of a reference herein shall not be construed as an admissionthat such is prior art to the present disclosure.

Having described the present disclosure in detail, it will be apparentthat modifications, variations, and equivalent embodiments are possiblewithout departing the scope of the present disclosure defined in theappended claims. Furthermore, it should be appreciated that all examplesin the present disclosure are provided as non-limiting examples.

Examples

The following non-limiting examples are provided to further illustratethe present disclosure. It should be appreciated by those of skill inthe art that the techniques disclosed in the examples that followrepresent approaches the inventors have found function well in thepractice of the present disclosure, and thus can be considered toconstitute examples of modes for its practice. However, those of skillin the art should, in light of the present disclosure, appreciate thatmany changes can be made in the specific embodiments that are disclosedand still obtain a like or similar result without departing from thespirit and scope of the present disclosure.

Example 1: Identification of Amino Acid Residues in the HR1 Mfn1 andMfn2 Domain that Influence Conformation

The following example shows that Mfn1 and Mfn2 conformation isinfluenced by a plurality of amino acid residues in the HR1 domain.

Mitochondria generate ATP that fuels neuronal activity. Mitochondrialdysfunction is implicated in chronic degenerative neurologicalconditions such as Alzheimer's, Parkinson's, and Huntington's diseases.Mitochondria fuse in order to exchange genomes and promote mutualrepair. The initial stages of mitochondrial fusion proceed through thephysiochemical actions of two closely related dynamin family GTPases,mitofusins (Mfn) 1 and 2. The obligatory first step leading tomitochondrial fusion is molecular tethering of two mitochondria viahomo- or hetero-oligomerization (in trans) of extended Mfn1 or Mfn2carboxyl termini. Subsequently, GTP binding to and hydrolysis by Mfn1 orMfn2 promotes irreversible physical fusion of the organellar outermembranes. The genetic neurodegenerative condition, Charcot Marie ToothDisease (type 2A) (CMT) or Hereditary motor and sensory neuropathy, iscaused by multiple loss-of-function mutations of Mfn2. The underlyingmechanism that causes this debilitating neuropathy is impairedmitochondrial fusion. Currently, because there are no pharmacologicalMfn agonists, there is no treatment for CMT.

Mfn1 and Mfn2 share a common domain structure, which was modeled usingI-TASSER and structural homology with bacterial dynamin-like protein,human Mfn1 and Arabidopsis thaliana dynamin-related protein (see e.g.,FIG. 1, top panel). The model shows how the first heptad repeat domain(HR1) interacts in an anti-parallel manner with the carboxyl terminalsecond heptad repeat (HR2) domain to restrain it and prevent itsextension into the cytosol, which can be necessary for mitochondrialtethering and fusion (see e.g., FIG. 1, top panel). The amino acidsnecessary for the HR1-HR2 interaction were identified as Met376, Ser378,His380, and Met 381 by first defining a minimal HR1-derived peptide thatcompetes with endogenous HR1-HR2 binding (see e.g., FIG. 2A-FIG. 2B) andfollowed by functional analyses of a complete series of alaninesubstituted peptides (see e.g., FIG. 2C). Based on these results,chemical peptido-mimetics could also mimic the 3-dimensional spatial andcharge characteristics of these critical amino acid side chains andwould have similar modulatory activity on mitochondrial fusion as theN-terminal mini-peptide (see e.g., Example 2).

Example 2: Peptido-Mimetic Compounds Influence Mfn1 and Mfn2Conformations

The following example describes peptide-mimetic compounds that influenceconformations of Mfn1 and Mfn2.

Mfn Agonist (Fusion-Promoting) Peptido-Mimetics

Forty-four candidate compounds were screened, 2 of which(1-[2-(benzylsulfanyl)ethyl]-3-(2-methylcyclohexyl)urea, designatedcompound A, and2-{2-[(5-cyclopropyl-4-phenyl-4H-1,2,4-triazol-3yl)sulfanyl]propanamido}-4H,5H,6H-cyclopenta[b]thiophene-3-carboxamide, designatedcompound B) induced mitochondrial elongation. Detailed analyses ofcompounds A and B were performed after purification by silica gelchromatography and structural validation by high performance liquidchromatography (HPLC) and mass spectroscopy (see e.g., FIG. 3). Acultured murine embryonic fibroblast assay system was used in whichmitochondrial elongation (an increase in aspect ratio) reflects enhancedmitochondrial fusion. Mitochondrial elongation evoked by compounds A andB (see e.g., FIG. 4A) was similar in cells expressing only Mfn2 (Mfn1null) or only Mfn1 (Mfn2 null), but did not occur in the absence of bothof their mitofusin targets (Mfn1/Mfn2 double null; see e.g., FIG. 4B).

Structure-activity relationships were interrogated to expand the pool ofMfn agonist compounds and to identify chemical analogs with differingpotencies for in vitro and in vivo comparative efficacy studies of CMT(see e.g., FIG. 5). Substitutions were evaluated for thecyclopenta[b]thiophene-3-carboxamide (green), sulfanyl-propanamido(purple), and 5-cyclopropyl-4-phenyl-4H-1,2,4-triazol-3-yl (red)moieties of Compound B. These derivatives are described in detail inTABLE 1 and TABLE 2.

TABLE 1 Mitofusin agonist peptido-mimetics 1-[2-(benzylsulfanyl)ethyl]-3-(2-methylcyclohexyl)urea MolPort-005- 680-744

3-{2-[(5-cyclopropyl-4- phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]ethyl}-1-(2- methylcyclohexyl)urea novel

2-[(5-cyclopropyl- 4-phenyl-4H-1,2,4-triazol-3- yl)sulfanyl]-N-(2-methylcyclohexyl)propanamide novel

2-({[2-(benzyl- sulfanyl)ethyl]carbamoyl}amino)-4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide novel

2-[2-(benzylsulfanyl)pro- panamido]-4H,5H,6H-cyclo-penta[b]thiophene-3-carboxamide novel

2-{2-[(5-cyclopropyl-4- phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]propanamido}- 4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide MolPort-004- 201-234

2-{2-[(5-cyclopropyl-4- phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamideMolPort-004- 059-486

2-(2-{[4-cyclopropyl-5-(1H- indol-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}propan- amido)-4H,5H,6H- cyclopenta[b]thio-phene-3-carboxamide MolPort-004- 214-844

2-{2-[(diphenyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propanamido}- 4H,5H,6H-cyclopenta[b]thiophene-3- carboxamide MolPort-005- 522-531

N-(4-chlorophenyl)-2-{2- [(5-cyclopropyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide MolPort-005- 784-050

N-benzyl-2-{2-[(5-cyclopropyl-4- ethyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide MolPort-005- 803-773

2-{2-[(5-cyclopropyl-4- ethyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamideMolPort-009- 869-122

N-benzyl-2-[2-({4-methyl-5- [(phenylcarbamoyl)methyl]-4H-1,2,4-triazol-3- yl}sulfanyl)acetamido]-4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide MolPort-002- 272-952

2-{[(3aS,6aS)-5-{5,7- dimethylpyrazolo[1,5- a]pyrimidine-2-carbonyl}-octahydropyrrolo[3,4- b]pyrrol-1-yl]methyl}-1- methyl-1H-imidazoleMolPort-023- 329-196

TABLE 2 Mitofusin agonist lower potency compounds 2-{2-[(4-benzyl-5-cyclopropyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propan- amido}-4H,5H,6H-cyclopenta[b]thio- phene-3- carboxamide MolPort- 004- 201-235

2-{2-[(4-phenyl-4H- 1,2,4-triazol-3- yl)sulfanyl]propan-amido}-4H,5H,6H- cyclopenta[b]thio- phene-3- carboxamide MolPort- 005-522-674

EC50 values for mitochondrial elongation by compounds A and B were100-200 nM, which is comparable to the prototype mini-peptide (Franco etal 2016 Nature 540: 74-79). When added in equal amounts, compounds A andB synergistically promoted mitochondrial elongation, with a combinedEC50 of ˜40 nM and a ˜25% greater maximal increase in mitochondrialaspect ratio (P<0.05 vs each compound alone; see e.g., FIG. 6A).

The mechanism for compound synergy was determined to be preferentialbinding of A and B to different phosphorylated forms of Mfn1 and Mfn2(see e.g., FIG. 6B, FIG. 6C): When Ser378 is replaced bynon-phosphorylatable alanine (A), cysteine (C), asparagine (N), orglycine (G) mini-peptide activity is abrogated because alternatesalt-bridge formation provokes α-helix destabilization of replacement ofHis380 by Leu379 and the HR1-HR2 interface (see e.g., FIG. 6D). Becausecompound B is hydrophobic (phenyl) at one end and polar (carboxamide) atthe other it mimics side chains presented by Val372/Met376/His381 (seee.g., FIG. 1, top panel). By contrast, compound A is hydrophobic (phenyland cyclohexyl) at both ends, which mimics the side chains presented tothe Mfn2 hydrophobic core after the conformational shift toVal372/Met376/Leu379.

Partial unwinding of the HR1 alpha helix and shifting of Met 380 forHis381 at the HR1-HR2 interacting interface is controlled by thephosphorylation status of Ser378 (see e.g., FIG. 6B). Thus, synergisticeffects of compounds A and B are likely the consequence of theirpreferential binding to different phosphorylated forms of Mfn1 and Mfn2.

The efficacy and synergy of the prototype Mfn agonist peptido-mimetics(small molecule mitochondrial fusion activators) were enhanced and theirspecificity modified by engineering novel chimeric compounds combiningoptimal features of the parental molecules (see e.g., FIG. 7, TABLE 1,TABLE 2). The ability of these compounds to repair mitochondrialfragmentation and neuronal pathology conditionally expressing a humanCharcot Marie Tooth disease mutation, Mfn2 T105M, was demonstrated (seee.g., FIG. 8, FIG. 9).

Example 3: HR1-HR2 Competition Binding Assay for Screening andEvaluating Mfn Peptido-Mimetic Targeting and Binding Affinity

The following example describes a HR1-HR2 competition binding assay forscreening and evaluating Mfn peptido-mimetic targeting and bindingaffinity.

The Mfn-derived fusion-promoting and -inhibiting mini-peptides(simulated to obtain the chemical Mfn agonists in TABLE 1 and TABLE 2)were modified from amino acid heptad repeats (HR) in the HR1 domain andpredicted to interact with their counterparts in the carboxyl terminusHR2 domain within the Mfn stalk region (see e.g., FIG. 1, top panel). Ahigh-throughput binding assay was designed whereby the target HR2peptide sequences, modified to include amino terminal 6×His tags and Glylinkers, were bonded to Ni-chelate resin (20 μg/ml) and used asimmobilized “receptor” for amino-FITC-tagged Mfn2 374-384 (agonistligand) in which the Ser analogous to Ser378 was replaced with Asp toconfer the negative charge essential for activity. For antagoniststudies the ligand was amino-FITC-tagged Mfn2 406-418. The FITC peptideligands are suspended at 1 mM in 30% DMSO, 70% water (to minimizespontaneous aggregation) and diluted into binding buffer (de-ionizedwater) to a final concentration of 25 μM in the presence or absence ofcompeting compound. Dose-dependent loss of resin-bound FITC signal (485nm excitation/538 nm emission) measured in a 96 well spectrofluorometerrepresents binding of compound to its HR2 target (see e.g., FIG. 10,FIG. 11). Either the ligand peptide or the receptor peptide can bemodified to represent mutations, variations, or posttranslationalmodifications of Mfn2. Target peptide-bound resin pre-incubated withFITC ligand in column form can be used for high throughput screening bymonitoring FITC in the eluate.

Amino acid sequences for Mfn agonist peptido-mimetic binding assaycomponents:

SEQ ID NO: 1: (NH3) HHHHHH-GGGG-AAMNKKIEVLDSLQSKAKLLRNKA-GG (COOH)(receptor)

SEQ ID NO: 2: (NH3) FITC-GGGG-AVRGIMDDLHMAAR-GG (COOH) (amino FITClabeled ligand) Amino acid sequences for Mfn antagonist peptido-mimeticbinding assay:

SEQ ID NO: 3: (NH3) HHHHHH-GGGG-LHAFTGSLEQQVQHSCNSG-GG (COOH) (receptor)

SEQ ID NO: 4: (NH3) FITC-GGGG-KQLELLAQDYKLRIKQ-GG (COOH) (amino FITClabeled ligand)

The system can be modified to contain the respective Mfn1 sequences ifspecific interrogation of both Mfn isoforms is desired.

Example 4: A Fret Assay for Screening and Evaluating Mfn Peptido-MimeticEffects on Mfn Conformation

The following examples describe a FRET assay for screening andevaluating Mfn peptido-mimetic effects on Mfn conformation.

The small molecules described herein enhance mitochondrial fusion bydestabilizing the folded conformation of Mfn1 or Mfn2, thus promotingextension of HR2 carboxyl termini that mediate mitochondrial tetheringby interacting in trans with similarly extended carboxyl termini of Mfn1or Mfn2 on neighboring mitochondria (see e.g., FIG. 12A). The Forsterresonance energy transfer (FRET) assay was designed to screen for andevaluate candidate agents of any chemical class, or molecules withspecific alternate compositions, including large libraries of syntheticor natural compounds.

The mechanism by which Mfn2 HR1 mini-peptides regulate Mfn1 and Mfn2activity is by directing Mfns into either an unfolded active or foldedinactive conformation, as demonstrated by a change in FRET signal ofMfn2 labeled with amino-terminal mCerulean and carboxyl terminal mVenus.This FRET system was limited by low transfection efficiency as aplasmid, an unacceptably poor signal to noise ratio, and the confoundinginfluences of Mfn GTPase activity.

These problems were solved by re-engineering the Mfn2 FRET probe afterdeleting the GTPase domain (A80-275) (which is dispensable to Mfnfolding/unfolding) and cloning it into an adenoviral vector for highefficiency expression. Briefly, mCerulean1 and mVenus were cloned ontothe 5′ and 3′ ends of a hMfn2 cDNA from which the entire GTPase domain(amino acids 80-275) was deleted (see e.g., FIG. 12C, top). Removal ofthe GTPase domain eliminates the need for adding GTPase inhibitors suchas GTPγS in the assay and increases the FRET signal to noise ratio. Thesequence-confirmed construct was sub-cloned into an adenoviral vectorfor expression in murine embryonic fibroblasts having differentmitofusin expression profiles (wild-type, Mfn1 null, Mfn2 null,Mfn1/Mfn2 double null) or other cell types. Forty-eight hours afteradenoviral transduction cells were pre-treated with the anti-fusionmini-peptide MP2 to increase FRET (1 μM, 1 hour; see e.g., FIG. 12C).Cells were then exposed to screening compound(s) for 1 hour in a 96 wellformat fluorescence plate reader or on the stage of a confocalmicroscope. FRET was analyzed as follows: mCerulean was excited at 436nm with emission at 480 nm. mVenus was excited at 500 nm with emissionat 535 nm. FRET was imaged with excitation at 436 nm and emission at 535nm. Data are represented as FRET signal/mCerulean signal. Increased FRETreflects folded Mfn2; loss of FRET reflects Mfn2 unfolding that favorsmitochondrial tethering and fusion.

The adeno-Mfn2 FRET A80-275 is expressed at near 100% efficiency at 50MOI in cultured murine embryonic fibroblasts (the cell of choice forfunctional screening of Mfn activity), and exhibits 5-fold greatersignal/noise that the original Mfn2 FRET probe. This system is useful in96 or 384 well formats for high-throughput screening of Mfn agonists(extinguishing of HR1 398-418 induced FRET) and antagonists (stimulationof baseline FRET or reversal of HR1 374-384 FRET suppression; see e.g.,FIG. 12).

Example 5: Rationally Designed Mitofusin Agonists Reverse In Vitro andIn Vivo CMT2A Mitochondrial Defects

This example describes the reversal mitochondrial defects in preclinicalmodels of Charcot Marie Tooth disease type 2A with MFN2 agonists andthat pharmacological disruption of intramolecular restraints in MFN2promotes mitochondrial fusion and trafficking in CMT2A neurons.

Mitofusins (MFNs) promote fusion-mediated mitochondrial content exchangeand subcellular trafficking. Mutations in MFN2 cause neurodegenerativeCharcot Marie Tooth Disease type 2A (CMT2A). Here, it has been shownthat MFN2 activity is determined by Met³⁷⁶ and His³⁸⁰ interactions withAsp⁷²⁵ and Leu⁷²⁷ and controlled by PINK1 kinase-mediatedphosphorylation of adjacent MFN2 Ser³⁷⁸.

Also shown here is that small molecule mimics of the peptide-peptideinterface of MFN2 disrupted this interaction, allosterically activatingMFN2 and promoting mitochondrial fusion. These first-in-class mitofusinagonists overcame dominant mitochondrial defects provoked in culturedneurons by CMT2A mutants MFN2 Arg⁹⁴→Gln⁹⁴ and Thr¹⁰⁵→Met¹⁰⁵, asdemonstrated by amelioration of mitochondrial dysmotility,fragmentation, depolarization, and clumping. A mitofusin agonistnormalized axonal mitochondrial trafficking within sciatic nerves ofMFN2 Thr^(105s)→Met¹⁰⁵ mice, promising a therapeutic approach for CMT2Aand other untreatable diseases of impaired neuronal mitochondrialdynamism and/or trafficking.

Mitochondria are organelles that generate a rich energy source forcells, which require their continuous subcellular redistribution viamitochondrial trafficking and mutual repair via mitochondrial fusion.Mitochondrial fusion and subcellular trafficking are mediated in part bymitofusin 1 (MFN1) and MFN2. Genetic mutations in MFN2 that suppressmitochondrial fusion and motility cause Charcot Marie Tooth Disease 2A(CMT2A), the most common heritable axonal neuropathy. Because notherapeutics exist that directly enhance mitochondrial fusion ortrafficking, this disease is unrelenting and irreversible.

Computational modeling based on the closed structure of bacterialdynamin-related protein (BDRP) and the more open structure of opticatrophy-1 suggested that MFN2 can change conformation according to howclosely the first and second heptad repeat (HR) domains interact (seee.g., FIG. 1). A closed conformation is fusion incompetent, whereas anopen conformation favoring mitochondrial fusion can be induced by acompeting peptide analogous to amino acids 367 to 384 within the MFN2HR1 domain. Amino acids controlling these events were identified, firstby truncation analysis to define the smallest fusion promotingminipeptide (residues 374 to 384) (see e.g., FIG. 2A-FIG. 2B), and thenthrough functional investigation of this minimal peptide by alanine(Ala) scanning. Substitution of Ala for Met³⁷⁶, Ser³⁷⁸, His³⁸⁰, andMet³⁸¹ which are highly conserved across vertebrate species (see e.g.,FIG. 13, FIG. 14) impaired minipeptide-stimulated mitochondrial fusion,as measured by an increase in the mitochondrial length/width (aspectratio) (see e.g., FIG. 2C). The structural model of human MFN2 in aclosed conformation on the basis of homology with BDRP predicted ahelical interaction between HR1 and HR2 domains, with alignment ofMet³⁷⁶ and His³⁸⁰ side chains in the HR1 domain with Leu⁷²⁷ and Asp725in the HR2 domain (see e.g., FIG. 1). This arrangement suggested thatMet³⁷⁶ and His³⁸⁰ stabilize the MFN2 HR1-HR2 interaction, potentiallyexplaining their critical function as defined by minipeptide Alascanning. By contrast, Ser³⁷⁸ was modeled as extending from thenoninteracting surface of the HR1 α helix (see e.g., FIG. 1), implying adifferent mechanism for its involvement in mitochondrial fusion.

To address whether Ser³⁷⁸ might be phosphorylated, Ser³⁷⁸ wassubstituted (with Ala, Cys, Asn or Gly) in the mini-peptide and it wasfound that phosphorylation and fusion activity were abrogated.Functionality was restored by substituting Asp to mimic phosphorylatedSer, or by inserting phospho-Ser [(p)Ser]itself (see e.g., FIG. 2D, FIG.15). Moreover, in an in vitro binding assay devoid of cellular kinasesthe Asp³⁷⁸-substituted minipeptide bound to its putative HR2 interactingdomain, whereas Ser³⁷⁸ and Ala³⁷⁸ minipeptides did not (see e.g., FIG.2E). Elimination of minipeptide binding by replacement of HR2 Leu⁷²⁴,Asp⁷²⁵, and Leu⁷²⁷ with Ala confirmed the HR1-HR2 interaction model (seee.g., FIG. 2F).

Nuclear magnetic resonance spectrometry of the minipeptides showed lowconformational stability with a propensity to form helical structures.Ser³⁷⁸ phosphorylation reduced the peptide dynamics most visibly forresidues Leu³⁷⁹ to Met³⁸¹, potentially changing amino acid side chainspresented to HR2 (see e.g., FIG. 16, FIG. 17). Indeed, recombinant MFN2mutations that replaced Ser³⁷⁸ with Asp (mimicking MFN2 Ser³⁷⁸phosphorylation) or substituted Ala for Met³⁷⁶ or His³⁸⁰ (disrupting theputative HR1-HR2 interaction controlled by Ser³⁷⁸ phosphorylation)impaired MFN2-stimulated mitochondrial fusion (see e.g., FIG. 18). Bycontrast, replacing MFN2 Ser³⁷⁸ with Ala (to prevent itsphosphorylation), or substitution Ala for neighboring Val³⁷², which wasnot important for HR1-HR2 interactions, did not depress MFN2-mediatedfusion (see e.g., FIG. 18).

MFN2 can be phosphorylated by mitochondrial PTEN-induced putative kinase1 (PINK1). Targeted mass spectrometry demonstrated phosphorylation ofMFN2 Ser³⁷⁸ as well as MFN2 Thr¹¹¹ and Ser⁴⁴² by PINK1 kinase (see e.g.,FIG. 2G; FIG. 19 and FIG. 20; TABLE 3), but not by software-nominatedG-protein receptor kinase 2 (see e.g., FIG. 21). MFN2 Ser³⁷⁸ mutantswere expressed with or without PINK1 in MFN1 and MFN2 doubly deficient(MFN1^(−/−), MFN2^(−/−)) cells. Fusion-defective mitochondria in thesecells were abnormally short at baseline, but forced expression ofwild-type (Ser³⁷⁸) MFN2 resulted in elongation from restoration offusion (see e.g., FIG. 2H, FIG. 22). Co-expression of PINK1 with MFN2,or mutational replacement of MFN2 Ser³⁷⁸ with Asp (which mimicsPINK1-mediated Ser³⁷⁸ phosphorylation) restrained MFN2-stimulatedelongation (see e.g., FIG. 2H, FIG. 22). By contrast, MFN2 Ala³⁷⁸ (whichcannot be phosphorylated) promoted mitochondrial fusion resistant toPINK1 suppression (see e.g., FIG. 2H, FIG. 22). The effects of MFN2Ser³⁷⁸ mutants were recapitulated in assays of fusion-mediatedmitochondrial content exchange (see e.g., FIG. 23).

TABLE 3 Fragmentation ions from tandem MS of MFN phosphopeptides.LIMDsLHMAAR¹ (m/z = 446.543) ion m/z (Theoretical) m/z (Observed) ppm y₁175.119 175.120 3.7 y₃ 317.193 317.194 1.4 y₄ 448.234 448.230 −9.0 y₅585.293 585.290 −3.6 y₆ 698.377 698.380 5.0 y₇-H₃PO₄ ⁺² 384.203⁺²384.203 0.7 y₈-H₃PO₄ 882.425 882.427 2.3 LIMDsLHMAAR-[¹³C₆][¹⁵N₄] (m/z =449.880) ion m/z (Theoretical) m/z (Observed) ppm y₁ 185.127 185.127 0.2y₂ 256.164 256.163 −4.3 y₃ 327.201 327.200 −3.1 y₄ 458.242 458.242 −0.7y₅ 595.301 595.300 −1.0 y₆ 708.385 708.382 −4.6 y₇-H₃PO₄ 777.406 777.404−3.7 y₈-H₃PO₄ 892.433 892.431 −2.1 y₉-H₃PO₄ 1023.474 1023.472 −1.7y₁₀-H₃PO₄ 1136.558 1136.549 −8.0 ¹The lower case single amino acidabbreviation indicates the phosphorylated residue.

Identification and De Novo Design of Small Molecule Mitofusin Agonists

A pharmacophore model was generated based on the interactions of HR1 andHR2 domains in the calculated structural model of Mfn2 in the closedconformation. The key features included hydrophobic interactionsinvolving Mfn2 HR1: Val372 and Met376, and aromatic interactions andhydrogen bonding involving Mfn2 HR1 His380. Although the pharmacophoremodel did not structurally model mitofusin agonist minipeptide HR1(367-384), it was noted that peptide residues Val6, Met10, and His14correspond to Mfn2 HR1: Val372, Met376 and His380. A library comprising˜14 million commercially available compounds was prepared in silico andevaluated using PHASE to fit these criteria. Top ranked hits wereclustered, and filtered based on pharmacological properties usingQikprop. The top 55 (see TABLE 4) commercially available small moleculesconforming to the model were selected for functional screening andpurchased in 1 mg aliquots. Each compound was dissolved to a stockconcentration of 10 mM in DMSO and applied to Mfn2 null MEFs overnightat a final concentration of 1 mM. Eleven of the library members were notsoluble in DMSO at the required concentration. The 44 fully solublecompounds were screened in groups of 6 at a time for cytotoxicity(calcein AM/ethidium homodimer staining; ThermoFisher LIVE/DEAD Assaycat #L3224) and fusogenicity (increase in mitochondrial aspect ratio;MitoTracker Orange staining) compared to cells treated overnight with 5mM of the parent HR1 367-384 mitofusin agonist peptide (positivecontrol) or vehicle (DMSO). Images were acquired by confocal microscopy.Each compound was scored for fusogenicity (see e.g., FIG. 24A) and %cell death (see e.g., FIG. 24B). Pharmacophore model fit generallycorrelated with actual fusogenic activity (Pearson correlationcoefficient r=0.214; see e.g., FIG. 24A, inset; TABLE 4).

TABLE 4 Fusogenicity screening results and characteristics of 55candidate mitofusin agonists (commercially sourced). Good- Aspect nessratio Fuso- of fit (MEAN ± genicity Rank IUPAC Name Structure SEM)* Rank1 2-{[(3aS,6aS)-5-{5,7- dimethylpyrazolo[1,5- a]pyrimidine-2-carbonyl}-octahydropyrrolo[3,4- b]pyrrol-1-yl]methyl}-1- methyl-1H-imidazole

9.0 ± 3.1  1 2 3-{[2-(1H-1,3-benzodiazol- 2-yl)ethyl]sulfanyl}-1-(3-fluorophenyl)pyrrolidine- 2,5-dione

6.9 ± 0.8  3 3 2-[({3-[5-methyl-2-(propan- 2-yl)phenoxy]propyl}sul-fanyl)methyl]-1H-1,3- benzodiazole

3.0 ± 0.4 37 4 2-[(4- methoxyphenyl)sulfanyl]-N- (1H-pyrazol-3-yl)propanamide

3.8 ± 0.4 22 5 1-[1-(4-chlorophenyl)- 1H,2H,3H,4H,9H-pyrido[3,4-b]indol-2-yl]-2- {[(4-fluorophenyl)- methyl]sulfanyl}ethan-1-one

4.7 ± 0.9 11 6 ethyl 4-methyl-2-(2-{5H- [1,2,4]triazino[5,6-b]indol-3-ylsulfanyl}butanamido)-1,3- thiazole-5-carboxylate

4.5 ± 0.5 13 7 2-({[4-oxo-6-(propan-2-yl)- 3H,4H,4aH,7aH-thieno[2,3-d]pyrimidin-2- yl]methyl}sulfanyl)-N- [(pyridin-2- yl)methyl]acetamide

3.8 ± 0.6 21 8 N-(3,4-dichlorophenyl)-2- {[2-(pyridin-2-yl)ethyl]sulfanyl}acetamide

2.8 ± 0.1 41 9 2-methyl-6-(2-{[(4-methyl- 1H-imidazol-5-yl)methyl]sulfanyl}ethyl)- 2H,6H,7H-pyrazolo[4,3- d]pyrimidin-7-one

2.8 ± 0.2 42 10 3-acetamido-N-(2-{[(4- methylphenyl)methyl]sul-fanyl}ethyl)adamantane-1- carboxamide

Not obtained Insol- uble 11 N-(2-{[(2- cyanophenyl)methyl]sulfan-yl}ethyl)-2-{methyl[1-(3- nitrophenyl)ethyl]amino}- acetamide

4.0 ± 0.5 16 12 N-(2,6-dimethylphenyl)-4- ({[3-(3-fluoro-4-methylphenyl)-1,2,4- oxadiazol-5- yl]methyl}sulfanyl)bu- tanamide

3.9 ± 0.5 20 13 5-methoxy-3′-(2- methylbenzoyl)-1-{[3-(trifluoromethyl)phenyl]- methyl}-1,2-dihydrospiro-[indole-3,2′-[1,3]thiazo- lidine]-2-one

3.5 ± 0.6 26 14 N-(2,6-dimethylphenyl)-4- ({[5-(propan-2-yl)-1,3-oxazol-2- yl]methyl}sulfanyl)butan- amide

3.5 ± 0.1 25 15 6-methyl-N-{[6-(4-methyl- 1,4-diazepan-1-yl)pyridin-3-yl]methyl}-2,3-dihydro-1- benzothiophene-2- carboxamide

4.0 ± 0.3 18 16 N-(2-{[(5-bromothiophen-2- yl)methyl]sulfanyl}ethyl)-1-(thiophene-2- carbonyl)piperidine-3- carboxamide

5.1 ± 0.2  9 17 3-{[1-(3,4-dimethylphenyl)- 1-oxopropan-2-yl]sulfanyl}-7-phenyl-7H,8H- [1,2,4]triazolo[4,3- a]pyrazin-8-one

Not obtained Insol- uble 18 1-(4-methylphenyl)-5-({1-[3-(4H-1,2,4-triazol- 3-yl)-1,2,4-oxadiazol-5-yl]ethyl}sulfanyl)-1H- 1,2,3,4-tetrazole

3.4 ± 0.3 27 19 5-methyl-N-{3-[(5-methyl- 1,3,4-thiadiazol-2-yl)sulfanyl]propyl}- 1H,4H,5H,6H,7H- pyrazolo[4,3-c]pyridine-3-carboxamide

3.1 ± 0.3 34 20 7-(4-bromophenyl)-3-{[1- (3,4-dimethylphenyl)-1-oxopropan-2-yl]sulfanyl}- 7H,8H-[1,2,4]triazolo[4,3- a]pyrazin-8-one

Not obtained Insol- uble 21 N-[2- (benzylsulfanyl)ethyl]oxane-2-carboxamide

3.3 ± 0.4 30 22 N-(2-{[(4- methylphenyl)methyl]sul- fanyl}ethyl)-1-[3-(trifluoromethyl)- [1,2,4]triazolo[4,3- b]pyridazin-6-yl]piperidine-4-carboxamide

Not obtained Insol- uble 23 1-cyclobutanecarbonyl-N- (2-{[(4-methyl-1H-imidazol-5- yl)methyl]sulfanyl}ethyl)- piperidine-4-carboxamide

2.9 ± 0.5 40 24 2-{[(2- {bicyclo[4.1.0]heptane-7- amido}pyridin-4-yl)methyl]sulfanyl}ethyl bicyclo[4.1.0]heptane-7- carboxylate

4.8 ± 1.0 10 25 N-(2-{[(3- chlorophenyl)methyl]sul- fanyl}ethyl)-5H,6H,7H,8H,9H- [1,2,3,4]tetrazolo[1,5- a]azepine-9-carboxamide

2.9 ± 0.2 38 26 2-{[4-benzyl-5-(morpholin- 4-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}-N-(2-oxo-2,3- dihydro-1H-1,3- benzodiazol-5- yl)propanamide

5.2 ± 0.2  8 27 1-[2-(benzylsulfanyl)ethyl]- 3-(2-methylcyclohexyl)urea

6.8 ± 0.6  4 28 1-{bicyclo[2.2.1]heptan-2- yl}-3-(2-{[(furan-2-yl)methyl]sulfanyl}ethyl)thio urea

3.7 ± 0.9 23 29 2-{[4-benzyl-5-(morpholin- 4-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}-N-(2,3-dihydro- 1,4-benzodioxin-6- yl)propanamide

6.0 ± 0.1  6 30 2-({2-[(morpholin-4- yl)methyl]quinazolin-4-yl}sulfanyl)-N-[3- (trifluoromethyl)phenyl]- propanamide

5.6 ± 0.6  7 31 2-{2-[(5-cyclopropyl-4- phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]propanamido}- 4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide

8.3 ± 2.3  2 32 2-{[4-(4-methylphenyl)-5- (morpholin-4-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}-N-[1- (propan-2-yl)-1H-pyrazol-5- yl]propanamide

4.1 ± 0.9 15 33 N-[4-(3,4-dihydro-2H-1,5- benzodioxepine-7-sulfonamido)phenyl]-2-[(4- methylphenyl)sulfanyl]- propanamide

Not obtained Insol- uble 34 5-methyl-2-{[1-(3-propyl- 1,2,4-oxadiazol-5-yl)ethyl]sulfanyl}-1H-1,3- benzodiazole

4.0 ± 1.0 17 35 (1S,4S)-2-(4-chloro-2- methoxy-5-methylphenyl)-5-{[1-(pyrimidin-2-yl)-1H- pyrrol-2-yl]methyl}-2,5-diazabicyclo[2.2.1]heptan- 3-one

Not obtained Insol- uble 36 1-(7-{3-[(4,6- dimethylpyrimidin-2-yl)sulfanyl]-2-methylpropyl}- 3-methyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8- yl)piperidine-4-carboxamide

Not obtained Insol- uble 37 2-{[2-(butan-2-yl)-3-oxo- 2H,3H-imidazo[1,2-c]quinazolin-5-yl]sulfanyl}- N-(3,5- dimethoxyphenyl)pro- panamide

3.2 ± 0.3 32 38 N-(5-methyl-1,2-oxazol-3- yl)-2-{[({4-[(1-phenylethyl)amino]phenyl}- carbamoyl)methyl]sulfanyl}- propanamide

Not obtained Insol- uble 39 N-(butan-2-yl)-2-{2-[(4-methylphenyl)sulfanyl]pro- panamido}benzamide

3.3 ± 0.4 29 40 N-ethyl-2-({12-ethyl-5-oxa- 1,10,11-triazatricyclo[6.4.0.0^(2,6)]do- deca-2(6),3,7,9,11-pentaen-9-yl}sulfanyl)-N-(3- methylphenyl)butanamide

Not obtained Insol- uble 41 5-[2-(benzylsulfanyl)ethyl]-3-(oxolan-3-yl)-1,2,4- oxadiazole

3.4 ± 0.6 28 42 2-[(4- bromophenyl)sulfanyl]-N- (2,3-dihydro-1,4-benzodioxin-6- yl)propanamide

3.2 ± 0.5 33 43 7-(3,4-dimethylphenyl)-3- {[1-(3,4-dimethylphenyl)-1-oxopropan-2-yl]sulfanyl}- 7H,8H-[1,2,4]triazolo[4,3- a]pyrazin-8-one

3.9 ± 0.8 19 44 9-oxo-N-(2-{[(thiophen-3- yl)methyl]sulfanyl}ethyl)-bicyclo[3.3.1]nonane-3- carboxamide

4.4 ± 0.6 14 45 N-(2H-1,3-benzodioxol-5- yl)-2-{[4-benzyl-5-(morpholin-4-yl)-4H-1,2,4- triazol-3- yl]sulfanyl}propanamide

2.5 ± 0.6 43 46 N-(cyclohexylmethyl)-2- ({2,8-dicyclopropyl-5,7-dioxo-5H,6H,7H,8H- pyrimido[4,5-d][1,3]diazin-4- yl}sulfanyl)propanamide

Not obtained Insol- uble 47 N-{[4- (dimethylamino)phenyl]-methyl}-2-({[(3- methylphenyl)carbamoyl]- methyl}sulfanyl)-N-(propan-2-yl)acetamide

4.6 ± 0.2 12 48 (1S,5R)-3-(6- methylpyridazin-3-yl)-6-[(pyridin-2-yl)methyl]-3,6- diazabicyclo[3.2.2]nonan-7- one

3.0 ± 0.4 36 49 4-[(4- methylphenyl)sulfanyl]-1- ({4H,5H,6H,7H-pyrazolo[1,5-a]pyrazin-2- yl}methyl)piperidine

2.9 ± 0.2 39 50 3-(2,5-dioxo-3-{[(E)-N-[(1- phenylethyl)imino]carbami-midoyl]sulfanyl}pyrrolidin-1- yl)benzoic acid

3.3 ± 0.0 31 51 2-{[(7,8-dimethyl-4-oxo-1,4- dihydroquinolin-2-yl)methyl]sulfanyl}-N-(2- ethoxyphenyl)acetamide

3.7 ± 0.6 24 52 2-{[2-oxo-2-(1,2,3,4- tetrahydroquinolin-1-yl)ethyl]sulfanyl}-N- phenylacetamide

2.4 ± 0.4 44 53 2-[(tert- butylcarbamoyl)amino]-2- oxoethyl2-[({4-oxo-5- phenyl-3H,4H-thieno[2,3- d]pyrimidin-2-yl}methyl)sulfanyl]acetate

6.5 ± 0.4  5 54 2-({2-[2-(3,5-dimethyl-1H- pyrazol-1-yl)ethyl]-8,9-dimethoxy- [1,2,4]triazolo[1,5- c]quinazolin-5-yl]sulfanyl)- N-(4-fluorophenyl)butanamide

Not obtained Insol- uble 55 N-(2,4-dimethylphenyl)-2-(2-{[(6-hydroxy-2,4-dioxo- 1,2,3,4-tetrahydropyrimidin-5-yl)[4-(propan-2- yl)phenyl]methyl]amino}-4-oxo-4,5-dihydro-1,3-thiazol- 5-yl)acetamide

3.1 ± 0.3 35 *Treatment with 1 μM compound.

Of nine compounds exhibiting apparent fusogenic activity on the initialscreen (defined as an increase in mitochondrial aspect ratio to >5 after24 h exposure to 1 mM compound), one (A8) was mildly cytotoxic andtherefore did not undergo further evaluation. The remaining eightcandidate fusogenic compounds were evaluated in a second series ofexperiments for their ability to provoke dose-dependent mitochondrialelongation. Fusogenicity of six compounds was confirmed, with EC₅₀values between ˜25 nM and 150 nM (see e.g., FIG. 25, TABLE 4). Twocompounds (D9 and A9) failed validation in the secondary screen.

The present results defining a minimal fusogenic HR1 peptide (see e.g.,FIG. 2B), identifying function-critical amino acids within theminipeptide (see e.g., FIG. 2C), and defining HR1-HR2 interacting aminoacids through binding assays (see e.g., FIG. 2E and FIG. 2F) suggestedthat the Mfn2 HR1-HR2 interaction model (see e.g., Example 1) wasimperfect, thus providing a likely reason for the poor correlationbetween in silico pharmacophore model fit of compounds B1 and A10 andtheir actual fusogenicity: Val372 was proven to be functionallydispensable and His380 paired with Asp725 rather than Lys720 asindicated in the original model. Moreover, the present studies revealedthat phosphorylation of Ser378 in both the mitofusin agonist peptide andintact Mfn2 protein can change amino acids presented to the HR1-HR2interface (see e.g., FIG. 11A); this key transitional feature was notpart of the initial model. Compounds A10 and B1 (which ranked 4^(th) and2^(nd) in fusogenicity, but 27^(th) and 31^(st) in fit to thepharmacophore model) and their chemosimilars conformed well to an Mfn2HR1-HR2 interaction model incorporating these biological findings, asdepicted in FIG. 1. These two compounds were therefore purified (seee.g., FIG. 3) and used in subsequent studies.

The ultimate goal was to design mitofusin agonists having optimalactivity profiles. (Here, a “fusogenic compound” is defined as promotingmitochondrial elongation without a clearly defined mechanism, while a“mitofusin agonist” is a fusogenic compound that binds to the Mfn2 HR2minipeptide target domain, promotes Mfn2 opening, and loses itsfusogenic activity when endogenous mitofusin proteins are not present).Molecular modeling of class A and B agonists assumed that theminipeptide a-helix is comprised of 3.6 amino acids per turn with a 1.4A pitch advance per amino acid, resulting in a distance of ˜5.4 Abetween amino acids of adjacent turns. Aliphatic backbones assumed adistance between single bonded carbons of 1.54 A. Structures werecreated or edited using Marvin JS at the MolPort website and availablechemical analogs (chemosimilars; TABLE 5) identified using the searchfunction and a similarity parameter of 0.5.

TABLE 5 Characteristics of 12 (6 each) class A and class B mitofusinagonists (commercially sourced). IUPAC ID Name Stucture pA3-phenyl-1-(4- phenylbutyl) urea

A1 1-[2- (benzylsul- fanyl)ethyl]-3- (2-methylcyclo- hexyl)urea

A2 3-(4- fluorophenyl)- 1-(4- phenylbutyl) urea

A3 3-(3-methyl- phenyl)-1-(4- phenylbutyl) urea

A4 3-(4- methylphenyl)- 1-(4-phenylbutyl) urea

A5 3-(2-methyl- phenyl)-1-(4- phenylbutyl) urea

pB 2-(4- phenylbutan- amido)- 4H,5H,6H- cyclopenta[b]- thiophene-3-carboxamide

B1 2-{2-[(5- cyclopropyl- 4-phenyl- 4H-1,2,4- triazol-3-yl)sulfanyl]pro- panamido}- 4H,5H,6H- cyclopenta[b]- thiophene-3-carboxamide

B2 2-[2- (phenylsulfa- nyl)acetamido]- 4H,5H,6H- cyclopenta[b]-thiophene-3- carboxamide

B3 3-acetamido- N-(2-{[(4- methylphen- yl)methyl]sul- fanyl}ethyl)ada-mantane-1- carboxamide

B4 2-{2-[(4- benzyl-5- cyclopropyl- 4H-1,2,4- triazol-3-yl)sulfanyl]pro- panamido}- thiophene-3- carboxamide

B5 N-benzyl-2- [2-({4- methyl-5- [(phenylcarb- amoyl)meth- yl]-4H-1,2,4-triazol-3- yl}sulfanyl)- acetamido]- 4,5,6,7- tetrahydro-1- benzothio-phene-3- carboxamide

Fusogenic activity of commercially available small-molecule candidatepharmacophores (TABLE 4), focusing on those having structures thatmimicked Ser³⁷⁸-phosphorylated (class A) and -unphosphorylated (class B)minipeptide amino acid side chains were assessed (see e.g., FIG. 5,TABLE 5). It was reasoned that simultaneous application of class A and Bagonists could enhance mitofusin by acting on both MFN2 Ser³⁷⁸phosphorylation states. Indeed, lead compounds (Cpd) A and B actedsynergistically to promote mitochondrial fusion (see e.g., FIG. 26;compare to FIG. 5C). Therefore, Cpd A and B functionality wereassimilated into a single molecule by creating Cpd A-B chimeras (seee.g., FIG. 11, FIG. 7, TABLE 6). The novel chimeric compoundsincorporated functional features (e.g., potency, specificity) of bothCpds A and B which were functionally synergistic because they acted ondifferent phosphorylated forms of MFN (see e.g., Example 2). ChimeraB-A/long (B-A/I) potently stimulated mitochondrial fusion inMFN2-deficient cells (see e.g., FIG. 11B), competed for minipeptidebinding at the MFN2 HR2 interaction site (see e.g., FIG. 11C), and wasas effective as the combination of Cpds A+B in reversing mitochondrialdysmorphology provoked by the CMT2A mutant, MFN2 Thr¹⁰⁵→Met¹⁰⁵ (MFN2T105M) (see e.g., FIG. 11D). Fusogenic effects of Cpd A were specificfor the Asp³⁷⁸ mutant of MFN2 that mimicked Ser³⁷⁸-phosphorylation,whereas Cpd B and chimera B-A/I were non-selective for the phosphomimicAsp³⁷⁸ and nonphosphorylatable Ala³⁷⁸ mutants (see e.g., FIG. 11E).Because they mimic WT MFN2 HR1 sequence and interact with HR2, mitofusinagonists evoked fusion to proportionally similar degrees in mitochondriaexpressing mutants of HR1 that are fusion deficient (see e.g., FIG. 11F;compare to FIG. 2H and FIG. 18). Small molecule mitofusin agonistsrequired endogenous MFN1 or MFN2 to promote mitochondrial fusion,exhibited no promiscuous activity for structurally related dynamin, anddid not compromise cell viability (see e.g., FIG. 27). On the basis offluorescence resonance energy transfer (FRET) analysis of MFN2 labeledat the N and C termini, mitofusin agonists promoted an open MFN2conformation favoring mitochondrial fusion, with a rank orderparalleling that for HR2 binding and mitochondrial fusion (see e.g.,FIG. 11G; compare to FIG. 11B and FIG. 11C), supporting allostericactivation.

Small molecule mitofusin agonists efficacy was shown in CMT2A model ofneuronal degeneration. In CMT2A, MFN2 mutants produce mitochondrial“fragmentation” (decreased aspect ratio) and loss of normal membranepolarization through dominant inhibition of normal mitofusins.Experiments using MFN1^(−/−), MFN2^(−/−)deficient murine embryonicfibroblasts (MEFs) showed that in the absence of normal mitofusins,small-molecule mitofusin agonists did not improve mitochondria of cellsexpressing the guanosine triphosphatase (GTPase)-crippled MFN2Arg⁹⁴→Gln⁹⁴ (R94Q) or Lys¹⁰⁹→Ala¹⁰⁹ (K109A) mutant (see e.g., FIG. 9A).However, mitofusin agonists corrected mitochondrial dysmorphology andreversed mitochondrial hypopolarization induced by these MFN2 mutantswhen MFN1 was present (MFN1^(+/+), MFN2^(−/−) MEFs) (see e.g., FIG. 9B).Mitofusin agonists also reversed mitochondrial fragmentation andhypopolarization in cultured neurons expressing (in addition toendogenous mitofusins) CMT2A mutants MFN2 R94Q (see e.g., FIG. 9C, FIG.9D) or MFN2 T105M (see e.g., FIG. 9E). Thus, mitofusin agonists do notrestore function of CMT2A MFN2 GTPase domain mutants. Rather, bydestabilizing the fusion-permissive open conformation of endogenous MFN1or MFN2, mitofusin agonists can overcome dominant suppression ofmitochondrial fusion by these disease-causing dysfunctional proteins.

Clinical CMT2A classically affects long nerves innervating the lower andupper limbs. It is unclear how a principal defect in mitochondrialfusion would cause length-dependent neuronal disease. Conversely,disruption of axonal mitochondrial transport would be predicted topreferentially impact cells requiring mitochondrial transport over thegreatest physical distance, such as the sciatic nerves originating inthe spine and terminating in the foot. MFN2 interacts with Miro/Miltonto promote mitochondrial trafficking in neurons, so the effects ofmitofusin agonism on murine neuronal mitochondrial trafficking weretested. Chimera B-A/I reversed mitochondrial “clumping” (formation ofstatic mitochondrial aggregates) and restored mitochondrial motility incultured neurons expressing the CMT2A mutant MFN2 T105M (see e.g., FIG.28A, FIG. 29). Mitochondrial hypopolarization and increased autophagy(see e.g., FIG. 28B, FIG. 30) and mitochondrial dysmorphology (see e.g.,FIG. 28C, FIG. 30) were concomitantly corrected. Thus, a small moleculemitofusin agonist enhanced organelle and cell fitness in CMT2A neuronsby promoting mitochondrial fusion and subcellular transport.

The concept of activating mitofusins to stimulate axonal mitochondrialtrafficking was evaluated in sciatic nerves of mice expressing the CMT2Amutant MFN2 T105M in vivo. In normal sciatic nerves ˜30% of axonalmitochondria exhibited robust bidirectional transport (see e.g., FIG.28, FIG. 31). Mitochondria of MFN2 T105M sciatic nerves were severelyhypomotile (see e.g., FIG. 28E, FIG. 32), but application of chimeraB-A/I to MFN2 T105M sciatic nerves restored mitochondrial motility towithin normal levels (see e.g., FIG. 28F, FIG. 32). Mobile mitochondriain WT and B-A/I-treated MFN2 T105M axons were smaller (see e.g., FIG.28G), supporting in vitro observations distinguishing betweenMFN2-mediated mitochondrial dysmotility and defective fusion in CMT2A.

Improvement in mitochondrial factors in ALS and HD patient-derivedfibroblasts treated with B-A/I was shown. Here, B-A/I enhancesmitochondrial structural defects, reduces mitochondrial ROS levels, andimproves mitochondrial membrane potential in ALS and HD patient-derivedfibroblasts and has no effect on fibroblasts from control subjects (seee.g., FIG. 28).

Here, it was found that PINK1 phosphorylation of MFN2 at Ser³⁷⁸ canalter the positions of Met³⁷⁶ and His³⁸⁰ (in the HR1 domain), whichnormally interact with HR2 domain amino acids to orchestrate MFN2toggling between conformations that modulate mitochondrial fusion. MFN2Ser³⁷⁸ phosphorylation (by PINK1 or other kinases) regulated thepositions of Met³⁷⁶ and His³⁸⁰ that interact with HR2 amino acids, thusdirecting MFN2 conformation and governing fusion. These findingsestablish a mechanistic basis for clinical observations that MFN2 Met³⁷⁶mutations to lie, Thr, and Val can cause CMT2A.

Based on molecular modeling and a detailed structural and functionalinterrogation of MFN2-derived minipeptides encompassing Met³⁷⁶, Ser³⁷⁸,and His³⁸⁰ small molecule mitofusin agonists were developed thatreversed mitochondrial dysmorphometry and normalized impaired mobilityevoked by 2 CMT2A MFN2 mutants. CMT2A is the prototypical clinicaldisorder of defective mitochondrial fusion, but impaired mitochondrialtrafficking may play as great a role as mitochondrial fragmentation inCMT2A axonal degeneration. Individuals with CMT2A express one mutantMFN2 allele in combination with one normal MFN2 allele and harbor twonormal MFN1 alleles. It is therefore possible that a therapeuticsubstrate for agonists to “supercharge” normal mitofusins and overcomedominant inhibition by MFN2 mutants. The observation that in vivomitochondrial dysmotility provoked by CMT2A mutants can be normalized bymitofusin agonists mechanistically links abnormal mitochondrialtrafficking in CMT2A to MFN2 dysfunction. Mitofusin agonists may alsohave therapeutic potential for neurological conditions other than CMT2A,such as Alzheimer's, Parkinson's, and Huntington's diseases, whereinmitochondrial dysmotility and fragmentation are contributing factors.

Materials and Methods

Cell Lines and Adenoviral Constructs

Wild-type MEFs were prepared from E10.5 c57/bl6 mouse embryos. SV-40 Tantigen-immortalized Mfn1 null (CRL-2992), Mfn2 null (CRL-2993) andMfn1/Mfn2 double null MEFs (CRL-2994) were purchased from ATCC. MEFswere subcultured in DMEM (4.5 g/L glucose) plus 10% fetal bovine serum,1×nonessential amino acids, 2 mM L-glutamine, 100 U/ml penicillin and100 ug/ml streptomycin.

Human Mfn2 Ser378 was mutated to Ala or Asp by site-directed mutagenesisusing the QuikChange Lightning kit (Agilent Technologies Inc.) andprimers:

Mfn2-S378D-fw 5′-cgactcatcatggacgacctgcacatggcggc-3′ (SEQ ID NO: 7)

Mfn2-S378D-rv 5′-gccgccatgtgcaggtcgtccatgatgagtcg-3′ (SEQ ID NO: 8)

Mfn2-S378A-fw 5′-gactcatcatggacgccctgcacatggcg-3′ (SEQ ID NO: 9)

Mfn2-S378A-rv 5′-cgccatgtgcagggcgtccatgatgagtc-3′ (SEQ ID NO: 10)

Mfn2 and its mutants were sub-cloned into adenoviral vector Type 5(dE1/E3) with RGD-fiber modification (Vector Biolabs) using BamHI/XhoI.All constructs were verified by Sanger DNA sequencing. Adeno-viral PINK1was purchased from Vector Biolabs. Immunoblotting used mouse anti-Mfn2(Abcam #ab56889, 1: 1000), anti-PINK1 (Sigma #P0076, 1: 500), andbeta-actin (Santa Cruz Biotechnology #sc-81178, 1:1000). Proteindetection and digital acquisition used peroxidase-conjugated anti mousesecondary antibody (Cell Signaling #7076S, 1:2500) and Western LightningPLUS ECL substrate (Perkin Elmer 105001EA) on a Li—COR Odysseyinstrument.

Peptide Studies

The C-terminal and N-terminal Mfn2 367-384Gly peptides and Alasubstituted variants of Mfn2 374-384 were chemically synthesized andintroduced into cells using TAT47-57 conjugation (ThermoFisherScientific). Except when indicated, 1 mM stocks in sterile water werediluted into culture media 1:1000 to achieve a final concentration of 1μM. Cells were treated overnight.

For Alanine scanning the following peptides were synthesized:

(NH3) GIADSLHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 11)

(NH3) GIMASLHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 12)

(NH3) GIMDALHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 13)

(NH3) GIMDSAHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 14)

(NH3) GIMDSLAMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 15)

The following peptides were synthesized for Ser378 substitution studies:

(NH3) GIMDSLHAAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 16)

(NH3) GIMDDLHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 17)

(NH3) GIMDS(p)LHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 18)

(NH3) GIMDGLHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 19)

(NH3) GIMDCLHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 20)

(NH3) GIMDNLHMAARGGYGRKKRRQRRR (COOH) (SEQ ID NO: 21)

Nuclear Magnetic Resonance (NMR) of HR1 Peptide Structure

Carboxyl terminal-amidated S378 parent and substituted peptide weresynthesized for NMR studies:

Mfn2-371-384 (378S)-AVRGIMDSLHMAAR (SEQ ID NO: 22)

Mfn2-371-384 (378S(p))-AVRGIMD[S(p)]LHMAAR (SEQ ID NO: 23)

Proton 2D NOESY and ¹⁵N-¹H heteronuclear single quantum coherenceoverlay spectra of the above peptides were recorded on 600 MHz BrukerAvance III spectrometer equipped with cryoprobe, at 15° C., pH 6, 50 mMNaCl, with each peptide at 2 mM concentration. Distance restraints werederived from observed NOE interactions between hydrogens within eachpeptide, and torsion angle restraints (φ and ψ) were derived from theobserved chemical shifts (for C, H and N nuclei). The calculations usedonly experimental data; no theoretical molecular dynamicssimulations/refinements were applied.

The helical structures/propensities in these peptides were not inferredor assumed from any single type of data. “Diagnostic” NOEs, inparticular dNN and dab(i, i+3), were present in 200 ms and 500 ms mixingtime H-H NOESY experiments, wherever signals could be resolved. Thestructural ensemble calculations used only restraints derived from NMRexperiments. Distance restraints were derived from observed NOEinteractions between hydrogens within each peptide, and torsion anglerestraints (f and y) were derived from the observed chemical shifts (forC, H and N nuclei).

Both ensembles show preponderance of helical conformation between378-383. These are more regular in phosphopeptide ensemble (see e.g.,FIG. 16C). Both ensembles show no regular conformation between 371-376,consistent with a lack of observed NOEs and values of chemical shiftscharacteristic for unstructured sequences. At the current level ofprecision, there is little difference between two ensembles in positionsof side chains for residues 379-383. The almost identical 13C/1Hchemical shifts of these methyl groups also suggest the similarity oftheir positions and local environments. However, the backbone amide(N—H) and Ca signals clearly show differences, beyond the obvious onecaused by phosphate esterification of serine. The amide signals shifteddown-field (to higher values), a characteristic observed when amidesform (or strengthen) hydrogen bonds within peptides. In general, thehelical secondary structure is often stabilized by a negatively chargedgroup “capping” the positive N-terminal end of the helix dipole. Here, aphosphorylation of Ser 378 can produce H-bonding for the amide ofLeu-379 and the negative phosphate can additionally stabilize thehelical turns following 379, providing an explanation for observeddown-field shifts (i.e., H-bonding induced) in amides of 380, 381 and382. MFN2 FRET for conformational studies

Mfn2 FRET probes contained N-termini-ceruleum and C-termini-mVenus fusedto the human (h) mitofusin protein as previously described. FRETanalyses were performed either on mitochondria isolated from Mfn1/Mfn2null MEFs expressing the WT hMfn2 FRET-hMfn2 protein or intact Mfn1/Mfn2null MEFs expressing WT or mutant Mfn2 FRET proteins (50 MOI). Forisolated mitochondria studies 65 μg of organelle protein was used foreach reaction in a total volume of 100 μl diluted in 10 mM Tris-MOPS (pH7.4), 10 mM EGTA/Tris, and 200 mM sucrose. 1 μM of mitofusin agonist inDMSO was added simultaneously with 2 μM mitofusin antagonist peptide,incubated in dark at room-temperature for 30 minutes, and FRET signalcorrected for Cerulean signal analyzed using a Tecan Safire IImulti-mode plate reader in polystyrene 96 well assay plate (Costar3916). Data acquisition was: FRET—Excitation 433/8 nm, Emission 528/8nm; Cerulean—Excitation 433/8 nm, Emission—475/8 nm. Isolatedmitochondria of non-infected cells were used to subtract background, andFRET signals were normalized to respective cerulean signals. The %changes in FRET/Cerulean provoked by mitofusin antagonist peptide andreversed by different mitofusin agonist small molecules were compared toMfn2-FRET mitochondria treated with water and DMSO, the vehicles for Mfnantagonist peptide and mitofusin agonist, respectively.

For FRET in intact cells, Mfn1/Mfn2 double null MEFs at 70% confluencewere infected with adenoviri expressing FRET-hMfn2, FRET-hMfn2 (S378A)or FRET hMfn2 (S378D) at 50 MOI. Two-days after transduction and 1 hourafter application of 1 μM Mfn2 antagonist mini-peptide MP2 to promotethe closed/inactive Mfn conformation, cells were released from tissueculture substrate with trypsin/EDTA, washed, and transferred to apolystyrene 96 well assay plate (Costar 3916; 20,000 cells/50 ml/well).Fifty-microliters of modified Krebs-Henseleit buffer containing DMSO(vehicle) or 1 μM mitofusin agonist was added with gentle agitation for10 min at room temperature. FRET and cerulean signals were assayed in a96-well plate reader (TriStar 2S LB 942, Berthold Technologies) with 1sec reading times at low sensitivity. Filters combinations are asfollows: FRET—Excitation 430/10, Emission 535/25; Cerulean—Excitation430/10, Emission—475/20. Signals from non-infected cells were used forbackground correction. FRET was normalized to the respective ceruleansignal for each well.

MFN2 Amino Terminal FLAG Epitope Unmasking Assay

HEK293 cells were transfected with wild-type or mutant MFN2 having anamino terminal FLAG epitope tag using Lipofectamine 3000 (Invitrogen)per the manufacturer's instructions. After 48 hours cells mitofusinagonists or DMSO vehicle were added at the indicated concentrations for1 hour (37° C.). Cells were harvested and proteins extracted usingInvitrogen cell extraction buffer supplemented with protease andphosphatase inhibitors (Roche). Proteins were quantified using theBradford assay (Biorad). Two mg aliquots of protein extract wereincubated in a final volume of 500 μl with 50 μl (bed volume) ofANTI-FLAG M2 Affinity Gel (Sigma) with gentle agitation for 2 hours at4° C. Beads were washed twice with 1 ml of cold PBS buffer and proteinswere eluted by adding 100 μl of reducing SDS sample buffer. Samples ofinput extract and immunoprecipitated proteins were size-separated onSDS-PAGE mini-gels and immunoblotted for MFN2.

HR1 Peptide-HR2 Target Binding Assay

Target HR2 peptide sequence modified to include amino terminal 6×Histags and Gly linkers, were bonded to Ni-NTA resin (4.4 μg/ml) (Quiagen)and used as immobilized “receptor” for amino-FITC-tagged Mfn2 374-384(ligand) in which the Ser analogous to Ser378 was replaced with Asp toconfer the negative charge essential for activity. FITC peptide ligandswere suspended at 1 mM in 30% DMSO, 70% water (to minimize spontaneousaggregation) and diluted into binding buffer (de-ionized water). For thedisplacement binding, 2.5 nmol of FITC labeled agonist peptide was usedin the presence or absence of different amounts of competing compounds.Resin-bound FITC signal (485 nm excitation/538 nm emission) measured ina 96 well spectrofluorometer (Spectramax M5e, Molecular Devices)represented binding to HR2 target. Competition binding isotherms wereplotted and IC₅₀ values calculated using Prism 7 (GraphPad).

Sequences for binding assay components are:

(NH3) HHHHHH-GGGG-AAMNKKIEVLDSLQSKAKLLRNKA-GG (COOH) (target) (SEQ IDNO: 24)

(NH3) HHHHHH-GGGG-AAMNKKIEVAASAQSKAKLLRNKA-GG (COOH) (target mutant)(SEQ ID NO: 25)

(NH3) FITC-GGGG-AVRGIMDSLHMAAR-GG (COOH) (FITC labeled Ser peptide) (SEQID NO: 26)

(NH3) FITC-GGGG-AVRGIMDDLHMAAR-GG (COOH) (FITC labeled Asp peptide) (SEQID NO: 27)

(NH3) FITC-GGGG-AVRGIMDALHMAAR-GG (COOH) (FITC labeled Ala peptide) (SEQID NO: 28)

Protein and Peptide Modeling

The hypothetical structures of human Mfn2 were developed using theI-TASSER Suite package. The putative closed conformation is based onstructural homology with bacterial dynamin-like protein (PDB: 2J69),human Mfn1 (PDB:5GNS), and Arabidopsis thaliana dynamin-related protein(PDB: 3T34). The putative open conformation was based on structuralhomology with human Opal, retrieved from the following structures: ratdynamin (PDB: 3ZVR), human dynamin 1-like protein (PDB: 4BEJ), and humanmyxovirus resistance protein 2 (PDB: 4WHJ). Minipeptide and proteinmodeling used PEP-FOLD3(http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/) and UCSFChimera, respectively.

Protein Alignment and Phylogenetic Analysis

Mfn2 orthologous sequences were retrieved from the Ensembl projectdatabase. Protein alignments were performed using Clustal Omega.

In Vitro PINK1-Mfn2 Phosphorylation Assay

In silico prediction of kinases that might phosphorylate Mfn2 Ser378 inthe peptide sequence AVRLIMDSLHMAARE used GPS 3.0(http://gps.biocuckoo.org). GRK2/bARK1 was the top hit (score of31.595), and GRK isoforms comprised 5 of the top 7 hits; ROCK kinase(score 15.919) and PKCa (score 11.48) were the other two hits. PINK1kinase is not represented at this site, and no other sites reported anylikely kinases for Mfn2 Ser378.

In vitro phosphorylation of Mfn2 by PINK1 and GRK kinases used amodified published protocol. Briefly, 20 mg of recombinant human Mfn2(expressed in HEK293 cells; OriGene: TP326143) plus 10-20 mg Triboliumcastaneum PINK1 (expressed in E. coli; Ubiquigent: 66-0043-050) or 10 mghuman GRK2 (Invitrogen: PV3361) were combined in kinase buffer (20 mMHepes pH 7.4, 10 mM DTT, 0.1 mM EGTA, 0.1 mM ATP and 10 mM MgCl2) andthe reactions allowed to proceed at 37° C. for 4 hours or overnight.

Mass Spectrometric Analysis of Mfn2 Phosphopeptides

Preparation of Peptides for Nano-LC-MS.

The in vitro kinase solution that contained 10 μg of Mfn2 was spiked (10μL) with a mixture of five carrier proteins (10 μg each). The mixtureconsisted of human apo-transferrin (Sigma, T4382), bovine α-casein(Sigma, C6780), bovine β-casein (Sigma, C6905), bovine ribonuclease(Sigma, R7884), and bovine albumin (Sigma A7030) in 100 mM Tris buffer,pH 7.6 with 4% SDS and 100 mM DTT. The sample was lyophilized overnightin a VirTis AdVantage Lyophilizer (SP Scientific).

Peptides were prepared using a modified filter-aided sample preparationmethod: dried sample was dissolved in 60 μL of Tris buffer, pH 7.6 thatcontained 4% SDS and 100 mM DTT and denatured by heating (95° C.) for 5min. The sample was then alkylated with 50 mM iodoacetamide (Sigma,A3221) for 1 h at room temperature in the dark. After the addition of 1ml of 50 mM ammonium bicarbonate buffer (pH 8.5) containing 8M urea (UA)and vortexing, equal volumes of the samples were transferred to twoYM-30 filter units (Millipore, Ref No. MRCF0R030) and spun for 14 min at10,000 rcf (Eppendorf, Model No. 5424). Filters were washed with 200 μlof UA and the spin-wash cycle was repeated twice. The sample was thenexchanged into digest buffer with the addition of 200 μl of ammoniumbicarbonate buffer, pH 8.5 (ABC) and centrifugation (11,000 rcf) for 10min. After transferring the upper filter unit to a new collection tube,80 μL of the ABC buffer was added and the sample was digested withtrypsin (1 μg) for 4 h at 37° C. The digestion was continued overnightafter another addition of trypsin. Filter units were then spun at 11,000rcf for 10 min with a subsequent filter washing step with 0.5 M NaCl (50μL) followed by centrifugation (14,000 rcf for 10 min). The digest wasthen extracted three times with 1 ml of ethyl acetate and acidified withtrifluoroacetic acid (TFA) (50%) to a final concentration of 1%. The pHwas <2.0 using pH paper. Solid phase extraction of the peptides wasperformed using sequential, robotic pipetting with C4 and porousgraphite carbon micro-tips (Glygen). The peptides were eluted with 60%acetonitrile in 0.1% TFA and pooled for drying in a Speed-Vac (ThermoScientific, Model No. Savant DNA 120 concentrator) after adding TFA to5%. The peptides were dissolved in 20 μL of 1% acetonitrile in water. Analiquot (10%) was removed for quantification using the PierceQuantitative Fluorometric Peptide Assay kit (Thermo Scientific, Cat. No.23290). The remaining sample was transferred to an autosampler vial(Sun-Sri, Cat. No. 200046), dried in the SpeedVac and dissolved in 2.7μL of 0.1% TFA.

Nano-LC-MS/MS Analysis of Phosphopeptides—

The samples were loaded (2.5 μL) at a constant pressure of 700 bar at100% of mobile phase solvent A (0.1% FA) onto a 75 μm i.d.×50 cmAcclaim® PepMap 100 C18 RSLC column (Thermo-Fisher Scientific) using anEASY nanoLC (Thermo Fisher Scientific). Before sample loading the columnwas equilibrated with 100% A using 20 μL at 700 bar. Peptidechromatography was initiated with A containing 2% B (100% ACN, 0.1% FA)for 5 min, then linear increased to 20% B over 100 min, to 32% B over 20min, to 95% B over 1 min and held at 95% B for 7 min, at a flow rate of300 nL/min. The data dependent mode analysis was performed with in theOrbitrap mass analyzer (Thermo-Fisher Scientific Q-Exactive™ Plus HybridQuadrupole-Orbitrap™ mass spectrometer) with a scan range of m/z=375 to1500 and a mass resolving power set to 70,000. Ten data-dependenthigh-energy collisional dissociations were performed with a massresolving power set to 17,500, a fixed lower value of m/z=100, anisolation width of 2 Da, and a normalized collision energy of 27. Themaximum injection time was 60 ms for parent-ion accumulations and 60 msfor product-ion analysis. The parent ions that were selected for MS2were dynamically excluded for 20 sec. The automatic gain control was setat a target ion value of 1e6 for MS1 scans and 1e5 for MS2 acquisition.Peptide ions with charge states of one or >8 were excluded for CIDacquisition.

Phosphopeptide data from the PINK kinase reactions were also acquired intargeted mode. The full-scan mass spectra were acquired by the Orbitrapmass analyzer with a scan range of m/z=350-2000 and a mass resolvingpower set to 70,000. The CID spectra were acquired at resolving power of17,500 with maximum table time of 120 ms. The loop count was set to 4and the isolation width was 2 Da. The acquisition of CID spectra weretriggered by an inclusion list of four m/z values for the +2 and +3charge state of the natural abundance phosphorylated andnon-phosphorylated peptide (see e.g., TABLE 3, above, for values). AnAGC target value of 3e6 was used for MS scans and 2e5 for MS/MS scans.The unprocessed LC-MS data were analyzed using SKYLINE (version 3.6.9).

The high-resolution ion chromatograms for the y ion series from the CIDphosphopeptide spectra shown in FIG. 2G were acquired during the LC-MSanalysis of the tryptic digest of human recombinant Mfn2 afterphosphorylation with PINK1. The corresponding chromatograms from thesynthetic, isotope-labeled phosphopeptide co-eluted with the PINK1product and all ions were observed with the same proportionalintensities in the CID spectra as shown in the adjacent stacked barcharts, confirming the sequence identity and phosphorylated residuelocation. The expected mass increment of 10 Da from the Arg-[13C6][15N4] residue was observed for all y ions in the CID spectra of thesynthetic phosphopeptide. The spectra from the PINK1 phosphopeptideproduct and the synthetic phosphopeptide were acquired from the triplycharged parent ions at m/z=446.543 and m/z=449.880, respectively. Thesite of phosphorylation was confirmed from the series of y ions withneutral losses of the phosphate moiety (H₃PO₄) that were observed asy8-H3PO4 (m/z=882.427), and y7-H3PO4+2 (m/z=384.203). The same ionseries was observed in the CID spectrum of the synthetic peptide withthe expected 10 Da mass increment, y8-H₃PO₄ (m/z=892.432) and y7-H₃PO₄(m/z=777.404). Using the synthetic phosphorylated and non-phosphorylatedpeptides, it was determined that the phosphopeptide consistently eluted9.5-10.5 min later in all LC-MS analyses. All tandem spectra that wereacquired from a precursor ion were also analyzed at m/z=446.543 for anyevidence of phosphorylation at Ser-378 in replicate PINK1 experiments,GRK phosphorylation experiments, and in a digest of the recombinant Mfn2protein without added kinase. Phosphopeptides with the Ser-378 site wereonly observed from the PINK1 phosphorylation experiments.

Dextran Uptake Assays of Dynamin Function

Wild-type MEFs (100,000 cells) were grown on cover slips. When theyreached 60% confluency they were washed with serum-free DMEM.Subsequently, cells were incubated in serum-free DMEM containing either1 μM compound A; B; B/A-L; dynasore (Calbiochem) or DMSO only (vehicle)for 30 min at 37° C. AF594-labelled 10,000 MW Dextran (Invitrogen) wasthen added to a final concentration of 0.5 mg/ml and incubated foradditional 10 min. at 37° C. Internalization was stopped by washingthree-times with ice-cold PBS. Residual dextran was removed by washingwith 0.1 M Na acetate, 0.05 M NaCl for 10 min. Samples were fixed in 4%PFA followed by confocal microscopy analysis.

Confocal Live Cell Studies of Mitochondria

Confocal imaging used a Nikon Ti Confocal microscope equipped with a60×1.3NA oil immersion objective. All live cells were grown on coverslips loaded onto a chamber (Warner instrument, RC-40LP) in modifiedKrebs-Henseleit buffer (138 mM NaCl, 3.7 mM KCl, 1.2 mM KH2PO4, 15 mMGlucose, 20 mM HEPES and 1 mM CaCl2) at room temperature.

Cells were excited with 408 nm (Hoechst), 561 nm (MitoTracker Green andCalcein AM, GFP), or 637 nm (TMRE, MitoTracker Orange, Ethidiumhomodimer-1, and AF594-Dextran) laser diodes. For mitochondrialelongation studies mitochondrial aspect ratio (long axis/short axis) wascalculated using automated edge detection and Image J software.Mitochondrial depolarization was calculated as % of green mitochondriavisualized on MitoTracker Green and TMRE merged images, expressed asgreen/(green+yellow mitochondria)×100.

Chemical Synthesis, Purification and Analyses of Novel Small MoleculeMitofusin Agonists

Four A-B chimeric molecules designed to incorporate differentcharacteristics of Cpds A and B (TABLE 6) were synthesized de novo:

TABLE 6 Characteristics of 4 novel, newly synthesized chimeric class A/Bmitofusin agonists (chimeras) Com- pound ID IUPAC Name Structure M.W.Formula Purity A-B/s 2-[2- (benzylsulfanyl)pro- panamido]-4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

360.4936 C18H20N2O2S2 98.8% B-A/s 2-[(5-cyclopropyl-4- phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]- N-(2- methylcyclohexyl)- propanamide

384.53822 C21H28N4OS 99.9% A-B/l 2-(3-(2-(benzyl- thio)ethyl)ureido)-5,6-dihydro-4H- cyclopenta[b]thio- phene-3-carboxamide

375.50824 C18H21N3O2S2 97.6% B-A/l 1-(2-((5-cyclopropyl-4-phenyl-4H-1,2,4- triazol-3- yl)thio)ethyl)-3-(2- methylcyclohexyl)-urea

399.55286 C21H29N5OS 99.9%

ChimeraB-A/I-(1-(2-((5-cyclopropyl-4-phenyl-4H-1,2,4-triazol-3-yl)thio)ethyl)-3-(2-methylcyclohexyl)urea)was synthesized by Enamine Ltd as a racemic mixture (see e.g., FIG. 33).Step A: 5-Cyclopropyl-4-phenyl-4H-1,2,4-triazole-3-thiol (1) (1 mmol)was dissolved in 1 mL of CH₃OH/H₂O (50:50), then NaOH (1 mmol) wasadded, stirred for 10 min, and 2-(boc-amino)ethyl bromide (2) (1 mmol)was added at 25° C. The reaction was allowed to stir for 3 hours thenpoured into 10 mL water. The precipitate was filtered and dried to get asolid. The crude product was dissolved in 10 ml of trifluoroacetic acid(TFA), and heated at 50° C. for 10 h to remove the solvent and 10 ml ofwater and NaOH (1 mmol) were added. The mixture was stirred at roomtemperature for 1 h, filtered, and washed with water (50 ml). Theresidue was purified using reversed phase high-performance liquidchromatography RP-HPLC. Yield: 52%. Step B:2-((5-Cyclopropyl-4-phenyl-4H-1,2,4-triazol-3-yl)thio)ethan-1-amine (3)(0.5 mmol) and 1,1′-carbonyldiimidazole (CDI) (1 mmol) were dissolved in0.6 ml CH₃CN, the mixture was kept at a temperature of 70° C. for 1 h,and then the 2-methyl-cyclohexylamine (4) (0.5 mmol) was added. Themixture was heated for 2 hours at 70° C., then filtered, and evaporated.The residue was purified using RP-HPLC to give the desired product as awhite solid; Purity: 99.99% (see e.g., FIG. 34A); Yield: 32%;C21H29N5OS; MW 399.5. Liquid chromatography with high-resolution massspectrometry using electrospray ionization LC-HRMS (ESI) with expectedm/z 399.25 showed exact mass found 400.2 [M+H]⁺ (see e.g., FIG. 34B).Chemical structure was confirmed by proton nuclear magnetic resonance(¹H NMR) and carbon-13 nuclear magnetic resonance (¹³C NMR) (see e.g.,FIG. 35). ¹H NMR (400 MHz, DMSO-d6) δ 7.60 (m, 3H), 7.48 (m, 2H), 5.95(dt, 1H), 5.81 (dd, 1H), 3.26 (q, 2H), 3.07 (t, 2H), 3.00 (m, 1H), 1.62(m, 4H), 0.99 (m, 10H), 0.81 (d, 2H), 0.75* (d, 1H). ¹³C NMR (126 MHz,CDCl₃) δ 157.45, 156.97, 149.14, 133.14, 129.74, 127.34, 53.83, 48.83,39.00, 34.12, 33.92, 32.69, 25.39, 25.30, 19.20, 7.15, 5.67.

Chimera B-A/s(2-((5-cyclopropyl-4-phenyl-4H-1,2,4-triazol-3-yl)thio)-N-(2-methylcyclohexyl)propanamide)was synthesized by Enamine as a racemic mixture (see e.g., FIG. 36):5-Cyclopropyl-4-phenyl-4H-1,2,4-triazole-3-thiol (1) (0.5 mmol) wasdissolved in 1 mL of CH₃OH, then KOH (0.5 mmol) was added, stirred for10 min, and then 2-chloro-N-(2-methylcyclohexyl)propanamide (2) (0.5mmol), was added at room temperature. The reaction was allowed to stirfor 3 hours then poured into 10 mL water. The precipitate was filteredand dried, then was purified using RP-HPLC to give the title compound asa light brown solid; Purity: 99.99% (see e.g., FIG. 37A); Yield: 43%;C21H28N4OS; MW 384.54. LC-HRMS (ESI): expected m/z 384.24, exact massfound 385.2 [M+H]⁺ (see e.g., FIG. 37B). Chemical structure wasconfirmed by ¹H NMR and ¹³C NMR (see e.g., FIG. 38): ¹H NMR (500 MHz,DMSO-d₆) δ 8.01 (dd, 1H), 7.60 (m, 3H), 7.45 (m, 2H), 4.27 (qd, 1H),3.14 (qd, 1H), 1.65 (m, 3H), 1.57 (m, 2H), 1.44 (d, 2H), 1.40 (d, 1H),1.16 (m, 4H), 0.93 (m, 3H), 0.86 (m, 2H), 0.78 (d, 2H), 0.71* (d, 1H).¹³C NMR (126 MHz, DMSO-d₆) δ 158.01, 139.15, 129.31, 128.75, 127.18,54.27, 49.26, 39.36, 38.56, 35.24, 34.61, 34.48, 31.88, 31.83, 25.88,25.79, 19.70.

Chimera A-B/I:(2-(3-(2-(benzylthio)ethyl)ureido)-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carboxamide)was synthesized by Enamine Ltd (see e.g., FIG. 39). Step A: Under anargon atmosphere, into a reaction vessel of2-amino-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carboxamide (1) (1.0mmol), potassium iodide (0.8 mmol), potassium carbonate (1.0 mmol),N,N-dimethylformamide (DMF) 1 mL and 2,2,2-trifluoroethyl chloroformate(2) (1.0 mmol) were added. The reaction vessel was heated to 80° C., andthe mixture was stirred for 12 hours. The reaction vessel was cooled toroom temperature, and ethyl acetate 100 mL was added. The organic layerwas washed with water (50 mL), saturated brine (50 mL), and dried oversodium sulfate. The sodium sulfate and the solvent were distilled off.Compound 3 was purified using RP-HPLC. Yield: 54%. Step B: To a solutionof 2 mmol of a 2,2,2-trifluoroethyl(3-carbamoyl-5,6-dihydro-4H-cyclopenta[b]thiophen-2-yl)carbamate (3) and2 mmol of an 2-(benzylthio)ethan-1-amine (4) in 2 mL of acetonitrile,0.2 mmol of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) was added. Thereaction mixture was heated at 80° C. for 4 h. Then 0.5-2 mL of waterwas added to the hot reaction mixture. The product precipitated from thesolution upon cooling to room temperature then filtered and concentratedin vacuum. The residue was purified using RP-HPLC to give the titlecompound as a brown solid. Purity: 97.56% (see e.g., FIG. 40A); Yield:51%; C18H21N3O2S2; MW 375.51; LC-HRMS (ESI): expected m/z 375.13, exactmass found 376.0 [M+H]⁺ (see e.g., FIG. 40B); Structure was confirmed by¹H NMR and ¹³C NMR (see e.g., FIG. 41): ¹H NMR (400 MHz, DMSO-d₆) δ10.87 (s, 1H), 7.88 (s, 1H), 7.31 (m, 6H), 6.47 (s, 1H), 3.76 (s, 2H),3.25 (q, 2H), 2.86 (t, 2H), 2.73 (t, 2H), 2.48 (m, 2H), 2.31 (p, 2H).¹³C NMR (126 MHz, DMSO-d₆) δ 167.20, 153.47, 151.94, 138.52, 128.88,128.84, 128.32, 107.82, 34.74, 30.66, 29.30, 28.22, 27.52.

Chimera A-B/s:(2-(2-(benzylthio)propanamido)-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carboxamide)was synthesized by Enamine Ltd as a racemic mixture (see e.g., FIG. 42):Phenylmethanethiol (1) (0.5 mmol) was dissolved in 1 mL of CH₃OH, thenethylbis(propan-2-yl)amine (0.55 mmol) was added, stirred for 10 min,and then2-(2-chloropropanamido)-4H,5H,6H-cyclopenta[b]thiophene-3-carboxamide(2) (0.5 mmol) was added. The reaction was allowed to stir at roomtemperature for 3 hours, and then poured into 10 mL water. Theprecipitate was filtered and dried, then was purified using RP-HPLC togive the title compound as a yellow solid; Purity: 98.76% (see e.g.,FIG. 43A); Yield: 37%; C18H20N2O2S2; MW 360.49; LC-HRMS (ESI): expectedm/z 360.12, exact mass found 361.2 [M+H]+(see e.g., FIG. 43B); Structurewas confirmed by 1H NMR and 13C NMR (see e.g., FIG. 44): ¹H NMR (500MHz, DMSO-d₆) δ 12.49 (s, 1H), 7.64 (s, 1H), 7.33 (d, 2H), 7.28 (t, 2H),7.22 (t, 1H), 6.70 (s, 1H), 3.83 (AB-system, 2H), 3.63 (q, 1H), 2.92 (t,2H), 2.79 (t, 2H), 2.36 (q, 2H), 1.40 (d, 3H). ¹³C NMR (126 MHz,DMSO-d₆) δ 168.77, 167.06, 148.07, 139.07, 137.35, 131.71, 128.91,128.37, 126.99, 111.30, 42.52, 34.88, 29.03, 28.22, 27.68, 17.57.

Purification Methods

Preparative HPLC

Purification was performed using HPLC (H₂O-MeOH; Agilent 1260 Infinitysystems equipped with DAD and mass-detectors. Waters Sunfire C18 OBDPrep Column, 100 Å, 5 μm, 19 mm×100 mm with SunFire C18 Prep GuardCartridge, 100 Å, 10 μm, 19 mm×10 mm) The material was dissolved in 0.7mL DMSO. Flow: 30 mL/min. Purity of the obtained fractions was checkedvia the analytical LCMS. Spectra were recorded for each fraction as itwas obtained straight after chromatography in the solution form. Thesolvent was evaporated in the flow of N₂ at 80° C. On the basis ofpost-chromatography LCMS analysis fractions were united. Solid fractionswere dissolved in 0.5 mL MeOH and transferred into pre-weighted markedvials. Obtained solutions were again evaporated in the flow of N₂ at 80°C. After drying, products were finally characterized by LCMS and ¹H NMRand 13C NMR.

Analytical Methods

HPLC/HRMS (ESI)

LC/MS analysis was carried out using Agilent 1100 Series LC/MSD systemwith DAD\ELSD and Agilent LC\MSD VL (G1956A), SL (G1956B)mass-spectrometer or Agilent 1200 Series LC/MSD system with DAD\ELSD andAgilent LC\MSD SL (G6130A), SL (G6140A) mass-spectrometer. All the LC/MSdata were obtained using positive/negative mode switching. The compoundswere separated using a Zorbax SB-C18 1.8 μm 4.6×15 mm Rapid Resolutioncartridge (PN 821975-932) under a mobile phase (A—acetonitrile, 0.1%formic acid; B—water (0.1% formic acid)). Flow rate: 3 ml/min; Gradient0 min—100% B; 0.01 min—100% B; 1.5 min—0% B; 1.8 min—0% B; 1.81 min—100%B; Injection volume 1 μl; Ionization mode atmospheric pressure chemicalionization (APCI); Scan range m/z 80-1000.

NMR

¹H and ¹³C NMR spectra were recorded at ambient temperature using BrukerAVANCE DRX 500; Varian UNITYplus 400 spectrometers.

Mouse Hippocampal Neuron Preparation, Culture, and Live Cell Imaging

Neonatal mouse hippocampal neurons were cultured from brains of one dayold Mfn2 T105M or non-transgenic sibling mouse pups as described. After10 days of differentiating culture neurons were infected with Adeno-Creto induce Mfn2 T105M expression or Adeno-βgal as a control (50 MOI).After an additional 72 hours mitofusin agonists or DMSO vehicle wereadded. For static confocal imaging neuronal mitochondria were labeledwith adenoviral-expressed mitoGFP plus TMRE. Autophagy was measured byLC3 aggregation in neurons infected with adenoviral LC3-GFP. Fortime-lapse studies of mitochondrial trafficking bi-cistronicAdeno-Cre/GFP marked Cre expression and mitochondria were labeled withadeno-mitoDsRed. Confocal live cell images were acquired with atime-lapse of 1 frame every 90 seconds for 1 hour.

HB9-Cre/Mfn2 T105M Mouse Creation and Sciatic Nerve Studies

All mouse procedures were approved by the Institutional Animal Care andUse Committee of Washington University in St. Louis.C57BL/6-Gt(ROSA)26Sortm1(CAG-MFN2*T105M)Dple/J (stock no. 025322 donatedby David Pleasure, University of California Davis) andB6.129S1-Mn×1tm4(cre)Tmj/J (here referred to as HB9-Cre; stock no.006600 donated by Thomas Jessel of Columbia University) were purchasedfrom The Jackson Laboratory. The HB9-Cre driver was bred onto the ROSA26flox-stop Mfn2 T105 transgene to induce Mfn2 T105M expression in motorneurons. Age- and sex-matched C57/b6 mice or mice carrying the MFN2 T105flox-stop transgene in the absence of Cre were studied as normalcontrols.

Sciatic nerves of 12-18 week old male or female MFN2 T105M mice wereremoved en bloc with the lumbar spine and axotomy at the tibial nerve,stained with TMEM (200 mM) for 30 minutes in prewarmed Neurobasal Mediumwithout phenol red (Thermo Fisher Scientific) at room temperature,washed, and maintained on the stage of a Nikon A1Rsi Confocal Microscopeat 37 degrees C. for time-lapse confocal studies. Images were acquiredwith a 40×oil immersion objective at 1 frame every 5 or 10 seconds forsequential 10 minute periods. Mitofusin agonist chimera B-A/I was addedafter the first 10 minute imaging period (final concentrations of 1 or 5mM) and nerve axons imaged for another 40 minutes. Because there was nodifference in mitochondrial trafficking or response to mitofusin agonistbetween male and female mice, the data were combined.

Statistical Methods

All data are reported as mean±SEM. Statistical comparisons (two-sided)used one-way ANOVA and Tukey's tests for multiple groups or Student'st-test for paired comparisons. p<0.05 was considered significant.

Cell Culture.

HD patient-derived fibroblast cell lines (GM04693 from 33-year-old malepatient and GM05539 from 10-year-old male patient) were purchased fromInvitrogen. ALS patient-derived fibroblasts (ALS 1: ND29509 from 55-yearold male patient having SOD1 mutation; ALS 2: ND30327 having FUS1mutation) and fibroblasts of control healthy individuals were purchasedfrom Coriell Institute, USA. All fibroblast cultures were maintained inMEM supplemented with 15% (v/v) FBS and 1% (v/v) penicillin/streptomycinat 37° C. in 5% CO2-95% air. Galactose media was used, to increasemitochondria-dependent metabolism oxidative phosphorylation. Humanfibroblasts were switched to grow for 48 h in DMEM deprived of glucoseand containing galactose (4.5 g/I), 1% FBS, 5 mM sodium pyruvate and 2mM L-glutamine for the studies.

Immunofluorescence.

Cells cultured in 8-well chamber slides were washed with cold PBS, fixedin 4% formaldehyde, and permeabilized with 0.1% Triton X-100. Afterincubation with 2% normal goat serum (to block nonspecific staining),fixed cells were incubated overnight at 4° C. with TOM20 antibody(1:500) (Santa Cruz, USA). Cells were washed with PBS and incubated for60 minutes with FITC-conjugated goat anti-rabbit IgG (1:500 dilution).The cells were then washed gently with PBS and counterstained withHoechst 33342 (1:10,000 dilution, Molecular Probes) to visualize nuclei.The coverslips were mounted with Slow-fade anti-fade reagent(Invitrogen), and images were acquired at 60×using an All-in-OneFluorescence Microscope BZ-X700 (Keyence).

Mitochondrial Health Assays.

Cells were incubated with tetra-methyl-rhodamine methyl ester (TMRM, 25nM, Invitrogen) in HBSS (Hank's balanced salt solution) for 30 min at37° C., per the manufacture's protocol, and the fluorescence wasanalyzed to measure mitochondrial membrane potential. All data werenormalized with respect to the fluorescence intensity of control cells.To determine mitochondrial ROS production, cells were treated with 5 μMMitoSOX™ Red, a mitochondrial superoxide indicator (Invitrogen) for 20min at 37° C., according to the manufacturer's protocol, andfluorescence was analyzed using SpectraMax M2e (Molecular devices).

Autophagy Assay.

Activation of autophagy was measured using the autophagy assay kit(Sigma Aldrich) according to the manufacturer's protocol, usingSpectraMax M2e (Molecular devices) (λex=333/λem=518 nm).

Example 6: Evolutionary Design of Small Molecule Mitofusin Agonists forIn Vivo Use

In vitro pharmacokinetic studies performed on the presently disclosedprototype small molecule mitofusin agonist, Regeneurin-S(S for thebackbone sulfur; chimera B-A/I from Example 5), revealed it to besoluble, highly protein bound, stable in plasma, but rapidly degraded byliver microsomes (see e.g., FIG. 45). The solubility of 1, 20, and 200mM solutions of compound in 50 mM phosphate buffer (pH 7.4) was assessedafter 24 shaking. Plasma protein binding was measured using equilibriumdialysis; % bound=(1-[free compound in dialysate]/[total compound inretentate])×100. Plasma stability of 2 mM compound in clarifiedfreeze-thawed plasma was assessed by LC-MS/MS of supernatants afterprotein precipitation; 120 min data are reported for studies including0, 10, 30, 60, and 120 min. Microsome stability of 1 mM compound inliver microsomes (0.5 mg/ml) after 0, 5, 10, 20, 30, 60 min. incubationwas assessed by LC/MS/MS of reaction extracts.

Regeneurin-S was considered to have three functional domainscorresponding to amino acid side chains of the prototype mitofusinagonist minipeptide it was designed to mimic: the methylated cyclohexanegroup corresponds to Mfn2 His380, the phenyl- andcyclopropyl-substituted triazol ring corresponds to Met376 and Val372,and the thioether backbone provides proper spacing (see Example 5) (seee.g., FIG. 46). According to this concept, a step-wise modification wasperformed of these functional domains to engineer subsequent generationsof agonists having different functional and pharmacokinetic properties.

It was initially posited that oxidation of the backbone sulfurcontributed to instability in the liver microsome assay. It was asked:(1) how does oxidation of this sulfur affect function (e.g.,Regeneurin-S fusogenic function)? and (2) could replacing the backbonesulfur increase stability in the liver microsome test? Thus, thesulfoxide and sulfone by chemical oxidation of the parent thioether wasgenerated (see e.g., FIG. 47 top), and the ether and carbon backbonevariants were synthesized de novo (see e.g., FIG. 47 bottom). Asillustrated in FIG. 47, neither oxidation nor substitution of thebackbone sulfur altered fusogenicity, consistent with the backboneacting simply as a spacer to properly position the active terminalgroups that mimic amino acid side chains of the prototype agonistpeptide. Nor did any of the chemical changes greatly increase molecularstability in the microsome test. However, Regeneurin-C/O, having thecarbon backbone and with tetrahydropyran substituted for the cyclohexylgroup, exhibited enhanced microsomal stability and improved (decreased)plasma protein binding.

These results showed that the backbone sulfur of Renegeurin-S wasneither function-critical, nor the basis for microsomal instability. Theresults also revealed a solution to microsomal instability evoked by themethylated cyclohexyl group. Recognizing that liver cytochrome P450enzymes oxidize aromatic rings, such as the phenyl group on the triazolring of the Regeneurin series of agonists, the structure-functionrelations of triazol ring group substitutions were next evaluated. Inthe pharmacophore model, the phenyl, cyclopropyl-substituted triazolring mimics the hydrophobic side chains of Mfn2 Met376 and Val372 (seee.g., FIG. 46). Thus, the mitochondrial fusogenicity of 70 commerciallyavailable chemical variants were compared, 17 of which differedexclusively in their triazol ring substitutions (see e.g., TABLE 7).Five compounds, all of which had a common chemical structure except fortriazol ring substitutions, were fusogenic (see e.g., FIG. 48); one ofthese was previously described (designated as “Cpd B” above).

TABLE 7 70 commercially available compounds evaluated. ID IUPAC NameStructure Cpd B 2-{2-[(5-cyclopropyl- 4-phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]- propanamido}-4H, 5H,6H-cyclopenta[b]-thiophene-3-carboxamide

1-G1 2-(2-{[4-(2-methylphenyl)- 5-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acet- amido)-4H,5H,6H- cyclopenta[b]thiophene-3-carboxamide

1-F9 2-(2-{[5-cyclopropyl-4- (prop-2-en-1-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acet- amido)-4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide

1-G11 2-{2-[(5-cyclopropyl-4- ethyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamido}- 4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-B1 2-{2-[(4-methyl-5-phenyl- 4H-1,2,4-triazol-3-yl]sulfanyl]acetamido}-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-F8 2-(2-{[4-cyclopropyl-5-(1H- indol-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]-thiophene-3-carboxamide

1-H11 2-{2-[(4-benzyl-5-cyclopropyl- 4H-1,2,4-triazol-3-yl)-sulfanyl]acetamido}-4,5,6,7- tetrahydro-1-benzothiophene- 3-carboxamide

1-F10 2-[2-({4-[(furan-2-yl)methyl]- 5-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl}sulfanyl)propanamido]- 4H,5H,6H-cyclopenta[b]-thiophene-3-carboxamide

1-F3 2-(2-{[5-methyl-4-(4- methylphenyl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]-thiophene-3-carboxamide

1-C12 2-(2-{[4-cyclopropyl-5-(thiophen- 2-yl)-4H-1,2,4-triazol-3-yl]-sulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]- thiophene-3-carboxamide

1-E12 2-(2-{[4-(2-methylphenyl)-5- (pyridin-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide

1-H2 2-(2-{[5-(4-chlorophenyl)-4- methyl-4H-1,2,4-triazol-3-yl}-sulfanyl]acetamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-B4 2-(2-{[4-methyl-5-(trifluoro- methyl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]- thiophene-3-carboxamide

1-H8 2-{2-[(diphenyl-4H-1,2,4- triazol-3-yl)sulfanyl]propan-amido}-4H,5H,6H-cyclo- penta[b]thiophene-3- carboxamide

1-D8 2-[2-({5-[(4-methoxyphenoxy)- methyl]-4-methyl-4H-1,2,4-triazol-3-yl}sulfanyl)propan- amido]-4H,5H,6H-cyclopenta-[b]thiophene-3-carboxamide

1-D3 2-(2-{[5-methyl-4-(4-methyl- phenyl)-4H-1,2,4-triazol-3-yl}sulfanyl]acetamido)-4,5,6,7- tetrahydro-1-benzothiophene-3-carboxamide

1-F7 2-(2-{[4-phenyl-5-(thiophen-2- yl)-4H-1,2,4-lriazol-3-yl]sul-fanyl}propanamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-H1 2-(2-{[4-(2-methylphenyl)-5- (pyridin-4-yl)-4H-1,2,4-triazol-3-yl}sulfanyl]acetamido- 4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-B8 2-(2-{[5-(2-methylfuran-3-yl)- 4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-C7 2-{2-[(4-benzyl-5-cyclopropyl- 4H-1,2,4-triazol-3-yl)sulfanyl]-propanamido}-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-D7 2-[2-({4-[(furan-2-yl)methyl]- 5-phenyl-4H-1,2,4-triazol-3-yl}sulfanyl)propanamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-D1 2-[2-({4-benzyl-5-[1-(dimethyl- amino)propyl]-4H-1,2,4-triazol-3-yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-E2 2-(2-{[4-(2-methoxyphenyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acet-amido)-4H,5H,6H-cyclopenta- [b]thiophene-3-carboxamide

1-F1 2-(2-{[5-(furan-2-yl)-4-phenyl- 4H-1,2,4-triazol-3-yl]sulfanyl}-acetamido)-4H,5H,6H-cyclo- penta[b]thiophene-3-carboxamide

1-H7 2-{2-[(5-benzyl-4-methyl-4H- 1,2,4-triazol-3-yl)sulfanyl]-acetamido}-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-D2 2-(2-{[4-(4-methoxyphenyl)- 4H-1,2,4-triazol-3-yl]sul-fanyl}acetamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-F2 2-(2-{[5-phenyl-4-(prop-2- en-1-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-B12 2-(2-{[4-(2-methoxyethyl)-5- (pyridin-4-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-A12 2-(2-{[4-phenyl-5-(piperidin-1- yl)-4H-1,2,4-triazol-3-yl]sul-fanyl]propanamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-H5 2-(2-{[4-(4-fluorophenyl)-5- (pyridin-4-yl)-4H-1,2,4-triazol-3-yl]sulfanyl]acetamido)- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

2-A5 2-{2-[(dimethyl-4H-1,2,4-triazol- 3-yl)sulfanyl]acetamido}-4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-E7 2-(2-{[4-methyl-5-(2-methyl- phenyl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]- thiophene-3-carboxamide

1-A1 2-(2-{[5-(4-chlorophenyl)-4- ethyl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-C8 2-[2-({4-phenyl-5-[(thiophen- 2-yl)methyl]-4H-1,2,4-triazol-3-yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-E10 2-(2-{[1-(2,3-dimethylphenyl)- 1H-imidazol-2-yl]sulfanyl}pro-panamido)-4H,5H,6H-cyclo- penta[b]thiophene-3-carboxamide

1-G10 2-(2-{5H,6H,7H,8H,9H-[1,2,4]tria-zolo[4,3-a]azepin-3-ylsulfanyl}acet- amido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide

1-G7 2-{2-[(1-benzyl-1H-imidazol-2- yl)sulfanyl]propanamido}-4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-C9 2-(2-{[4-methyl-5-(2-methylfuran- 3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-G8 2-{2-[(4-phenyl-4H-1,2,4-triazol- 3-yl)sulfanyl]propanamido}-4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-E8 2-(2-{[1-(3-fluorophenyl)-1H- imidazol-2-yl]sulfanyl}pro-panamido)-4H,5H,6H-cyclo- penta[b]thiophene-3-carboxamide

1-D6 2-(2-{[5-(furan-2-yl)-4-phenyl- 4H-1,2,4-triazol-3-yl]sulfanyl]-propanamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-B7 2-[2-({4-methyl-5-[(thiophen-2- yl)methyl]-4H-1,2,4-triazol-3-yl}sulfanyl)propanamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-C5 2-(2-{[4-(2-methylphenyl)-4H- 1,2,4-triazol-3-yl]sulfanyl}acet-amido)-4H,5H,6H-cyclopenta- [b]thiophene-3-carboxamide

1-D12 2-(2-{5H,6H,7H,8H,9H- [1,2,4]triazolo[4,3-a]azepin-3-ylsulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]- thiophene-3-carboxamide

2-A2 2-{2-[(dicyclopropyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acet-amido}-4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide

1-G2 2-{2-[(diphenyl-4H-1,2,4-triazol- 3-yl)sulfanyl]acetamido}-4,5,6,7-tetrahydro-1-benzothiophene-3- carboxamide

1-E5 2-{2-[(5-cyclopropyl-4-phenyl- 4H-1,2,4-triazol-3-yl)sulfanyl]-acetamido}-4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide

1-A10 2-(2-{5H,6H,7H,8H,9H- [1,2,4]triazolo[4,3-a]azepin-3-ylsulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]thio- phene-3-carboxamide

1-D10 2-(2-{[5-(2-methylfuran-3-yl)-4- phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-F5 2-{2-[(5-cyclopropyl-4-ethyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acet-amido}-4,5,6,7-tetrahydro-1- benzothiophene-3-carboxamide

1-F11 2-(2-{[4-phenyl-5-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl]acet- amido)-4H,5H,6H-cyclopenta[b]-thiophene-3-carboxamide

1-G6 2-[2-({4-cyclopropyl-5-[(thiophen- 2-yl)methyl]-4H-1,2,4-triazol-3-yl}sulfanyl)propanamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-G3 2-(2-{[4-phenyl-5-(pyridin-3- yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide

1-F6 2-[2-({5-[1-(dimethylamino)ethyl]- 4-(4-fluorophenyl)-4H-1,2,4-triazol-3-yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-A8 2-{2-[(5-benzyl-4-ethyl-4H- 1,2,4-triazol-3-yl)sulfanyl]-propanamido}-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-H3 2-{2-[(5-methyl-4-phenyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acet-amido}-4H,5H,6H-cyclo- penta[b]thiophene-3- carboxamide

1-E1 2-(2-{[5-cyclohexyl-4-(prop- 2-en-1-yl)-4H-1,2,4-triazol-3-yl}sulfanyl]acetamido)- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-C6 2-[2-({5-[(1,1-dioxo-1λ⁶-thiolan- 3-yl)methyl]-4-methyl-4H-1,2,4-triazol-3-yl}sulfanyl)- acetamido]-4,5,6,7-tetrahydro-l-benzothiophene-3-carboxamide

1-A3 2-(2-{[5-(4-fluorophenyl)-4- methyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta[b]- thiophene-3-carboxamide

1-H6 2-{2-[(5-benzyl-4-methyl-4H- 1,2,4-triazol-3-yl)sulfanyl]propanamido}- 4H.5H.6H-cyclopenta[b]-thiophene-3-carboxamide

1-E9 2-[2-({5-[(1,1-dioxo-1λ⁶-thiolan-3- yl)methyl]-4-methyl-4H-1,2,4-triazol-3-yl}sulfanyl)propanamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-A6 2-(2-{[4-ethyl-5-(2-methyl- furan-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}propanamido)- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-C4 2-{2-[(4-phenyl-4H-1,2,4- triazol-3-yl)sulfanyl]acetamido}-4H,5H,6H-cyclopenta- [b]thiophene-3-carboxamide

1-F4 2-(2-{[4-(2-methoxyphenyl)- 5-methyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)-4,5,6,7- tetrahydro-1-benzothiophene-3-carboxamide

1-D9 2-[2-({5-[(1,1-dioxo-1λ⁶- thiolan-3-yl)methyl]-4-methyl-4H-1,2,4-triazol-3- yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta-[b]thiophene-3-carboxamide

1-A2 2-(2-{[4-cyclopropyl-5-(2- fluorophenyl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetamido)- 4H,5H,6H-cyclopenta-[b]thiophene-3-carboxamide

2-A5 2-{2-[(dimethyl-4H-1,2,4- triazol-3-yl)sulfanyl]acet-amido}-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-C11 2-[2-({4-methyl-5-[(thiophen- 2-yl)methyl]-4H-1,2,4-triazol-3-yl}sulfanyl)acetamido]- 4H,5H,6H-cyclopenta[b]thio-phene-3-carboxamide

1-C2 2-{2-[(4-benzyl-5-methyl-4H- 1,2,4-triazol-3-yl)sulfanyl]acetamido}-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

1-A7 2-(2-{[1-(4-methoxyphenyl)-1H- imidazol-2-yl]sulfanyl}-propanamido)-4H,5H,6H- cyclopenta[b]thiophene-3- carboxamide

Two Cpd B chemosimilars, 1-G11 and 1-B1, were more potent and hadgreater resistance to liver microsomal degradation than their parent,Cpd B (see e.g., FIG. 49, TABLE 7). Because compound 1-G11 lackedaromatic groups on the triazol ring, having replaced an ethyl group forthe phenyl group in Cpd B, the next series of chemical modificationsintroduced this configuration; this series of agonists were designatedMitolityns. Mitolityn-1 simply substituted an ethyl group for the phenylgroup of the triazol ring in Regeneurin-C, retaining the rest of itsstructure (see e.g., FIG. 50).

Because it was reasoned that the methylated cyclohexane group might alsobe susceptible to oxidation by liver cytochrome P450, additionalmodifications were engineered to remove the cyclohexane methyl group(Mitolityn-2), replace the methylated cyclohexane ring with a methylatedtetrahydropyran ring (Mitolityn-3), and replace the methylatedcyclohexane with an unmethylated tetrahydropyran ring (Mitolityn-4;corresponding to replacing the triazol phenyl group of Regeneurin C/Owith an ethyl group. Finally Mitolityn-3 and -4 with methyl rather thanethyl groups on the triazol ring were synthesized (see e.g., FIG. 50).The Mitolityn series of compounds were then assayed for fusogenicity(increase in aspect ratio) and liver microsome stability (see e.g., FIG.50).

Neither of the lead compounds in the presently disclosed structurallydistinct series of mitofusin agonists, Mitolityn-4 or Regeneurin-C,exhibited cytotoxicity up to drug concentrations of 100 mM, which ismore than 4 orders of magnitude greater concentration than their EC50 tostimulate mitochondrial fusion (see e.g., FIG. 51).

Notwithstanding similar fusogenic efficacies and lack of cytotoxicity,in vitro pharmacokinetic studies of the lead compounds revealed markeddifferences in plasma protein binding, liver microsome stability, andparallel artificial membrane permeability assay (PAMPA) (see e.g., FIG.52). Like prototypical Regeneurin-S (see e.g., FIG. 2), Regeneurin-C washighly bound to plasma proteins, but rapidly degraded by livermicrosomes, showed excellent passive diffusion across a lipid-infusedartificial membrane (PAMPA), but was actively transported by P-gp/MDR1.These features suggested that this compound might not be effectivelydelivered to the central and peripheral nervous systems in vivo.Mitolityn-4 exhibited the reciprocal of these features, with low plasmaprotein binding, stability in the liver microsome assay, no passivediffusion across lipid membrane and therefore no reverse transport byP-gp. These features were also not conducive to central and peripheralnervous system delivery. Regeneurin C/O, however, had intermediatefeatures, being modestly bound to plasma proteins, stable in the livermicrosome assay, and exhibiting intermediate passive permeability andP-gp mediated reverse transport.

Preliminary in vivo pharmacokinetic studies revealed that the presentlydisclosed mitofusin agonists compounds are eliminated from thecirculation within 2 hours of IV, IP, or IM administration (see e.g.,FIG. 53); IM administration provided the longest plasma half-time andbioavailability. For Regeneurin-C that is ˜90% plasma protein bound (seee.g., FIG. 52), drug was undetectable 2 hours after IM administration,reflecting virtual absence of free drug. However, for Mitolityn-4 thatis only 11.2% plasma protein bound in the mouse (see e.g., FIG. 52),total plasma drug concentration 2 hours after IM administration was 7.5ng/ml, or ˜6.66 ng/ml (˜20 nM) free drug concentration, which is stillseveral-fold greater than its EC50 of ˜3 nM (see e.g., FIG. 53). Thus,in vivo efficacy for Mitolityn-4 was expected, but not Regeneurin-C, forat least 2 hours after a single IM injection.

The presently disclosed step-wise chemical evolution from firstgeneration mitofusin agonists, Regeneurin-S (aka chimera B-A/I),Regeneurin-C, and Regeneurin-C/O, to second generation Mitolityns-4 and-6 revealed that the oxygen atom in the tetrahydropyran ring improved invitro microsomal instability and reduced plasma protein binding relativeto the parent 2-methylcyclohexyl group. Moreover, the structure-activityrelationships of members of the Regeneurin and Mitolityn series ofcompounds refined the understanding of how these molecules mimic theprototype mitofusin agonist peptide: the cyclopropyl group extendingfrom the triazol ring of Mitolityn-4 provides a hydrophobic interactionlike that of Val372, whereas the tetrahydropyran ring on the oppositeend of the molecule mimics both a ringed structure and hydrogen bondacceptor activity of His380.

Here, the optimization of Regeneurin C/O is shown, enhancing itsstability and introducing features that will help it cross the BBB, bymodifying it as shown in FIG. 54; these methods can be used to furthersynthesize optimized Regeneurins. Moreover, it is presently thought thatsubstitution of the 3-cyclopropyl group on the 2,4,5 triazol ring with astructurally distinct moiety having similar hydrophobic characteristicsshould preserve the functional activity of the molecule, retain lowplasma protein binding and microsomal stability, but have greaterlipophilicity for blood- and nerve-brain barrier permeability. Thisapproach was tested by synthesizing three additional mitofusin agonistcandidates having a 3-phenyl replacing the 3-cyclopropyl group in theMitolityn 2,4,5 triazol ring structure; this new series of Mfn agonistsare called Fusogenins (see e.g., FIG. 55).

TABLE 8 Novel Regeneurin agonists. Compound ID IUPAC Name Structure M.W.(g/mol) Formula Regeneurin-C 1-(3-(5-cyclopropyl- 4-phenyl-4H-1,2,4-triazol-3-yl)propyl)-3- (2- methylcyclohexyl)urea

381.52 C22H31N5O Regeneurin-O 1-(2-((5-cyclopropyl- 4-phenyl-4H-1,2,4-triazol-3- yl)oxy)ethyl)-3-(2- methylcyclohexyl)urea

383.49 C21H29N5O2 Regeneurin- C/O 1-(3-(5-cyclopropyl-4-phenyl-4H-1,2,4- triazol-3-yl)propyl)-3- (tetrahydro-2H-pyran-4-yl)urea

369.47 C20H27N5O2 Regeneurin- SO 1-(2-((5-cyclopropyl-4-phenyl-4H-1,2,4- triazol-3- yl)sulfinyl)ethyl)-3- (2-methylcyclohexyl)urea

415.55 C21H29N5O2S Regeneurin- SO2 1-(2-((5-cyclopropyl-4-phenyl-4H-1,2,4- triazol-3- yl)sulfonyl)ethyl)-3- (2-methylcyclohexyl)urea

431.56 C21H29N5O3S

TABLE 9 Novel Mitolityn agonists. Compound M.W. ID IUPAC Name Structure(g/mol) Formula Mitolityn-1 1-(3-(5- cyclopropyl-4- ethyl-4H-1,2,4-triazol-3- yl)propyl)-3-(2- methylcyclohexyl) urea

333.47 C18H31N5O Mitolityn-2 1-cyclohexyl-3-(3- (5-cyclopropyl)-4-ethyl-4H-1,2,4- triazol-3- yl)propyl)urea

319.45 C17H29N5O Mitolityn-3 1-(3-(5- cyclopropyl-4- ethyl-4H-1,2,4-triazol-3- yl)propyl)-3-(3- methyltetrahydro- 2H-pyran-4- yl)urea

335.44 C17H29N5O2 Mitolityn-4 1-(3-(5- cyclopropyl-4- ethyl-4H-1,2,4-triazol-3- yl)propyl)-3- (tetrahydro-2H- pyran-4-yl)urea

321.42 C16H27N5O2 Mitolityn-5 (Renamed after Fusogenin- 4a) 1-(3-(5-cyclopropyl-4- methyl-4H-1,2,4- triazol-3- yl)propyl)-3-(3-methyltetrahydro- 2H-pyran-4- yl)urea

321.43 C16H27N5O2 Mitolityn-6 (Renamed after Fusogenin- 3a) 1-(3-(5-cyclopropyl-4- methyl-4H-1,2,4- triazol-3- yl)propyl)-3- (tetrahydro-2H-pyran-4-yl)urea

307.4  C15H25N5O2

TABLE 10 Novel Fusogenin agonists. Compound M.W. ID IUPAC Name Structure(g/mol) Formula Fusogenin-1 1-(3-(4-methyl-5- phenyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(2- methylcyclohexyl) urea

355.49 C20H29N5O Fusogenin-3 1-(3-(4-methyl-5- phenyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(tetrahydro-2H- pyran-4-yl)urea

343.43 C18H25N5O2 Fusogenin-4 1-(3-(4-methyl-5- phenyl-4H-1,2,4-triazol-3-yl)propyl)- 3-(3- methyltetrahydro- 2H-pyran-4-yl)urea

357.46 C19H27N5O2

Example 7: Pre-Clinical Studies Evaluating the Potential Efficacy ofMitofusin Agonists in CMT2A and Other Chronic NeurodegenerativeSyndromes

The following example shows mitofusin agonist effects on mitochondrialpathology in primary fibroblasts from human neurodegenerative diseasepatients.

High neuronal metabolic activity makes the neurological system uniquelysusceptible to genetic mitochondrial damage. Oxidative stress isfrequently invoked as the mechanism linking mitochondrial dysfunction toneurological diseases, but defective mitochondrial transport in longperipheral axons may contribute to neuronal vulnerability. For example,bioenergetic support of neuronal maintenance, repair and regenerationrequires mitochondrial redistribution to sites of degeneration.Accordingly, it was examined whether the facilitory effects of thepresently disclosed small molecule mitofusin agonist, Regeneurin-C, onmitochondrial trafficking, fusion, and polarization status would improvemitochondria fitness in primary fibroblasts from human patients with avariety of mutations causing Amyotrophic lateral sclerosis (3 SOD1 genemutations) Huntington's (HD gene CAG repeat numbers 40, 57, and 66),Parkinson's (Parkin, PINK, and LRRK2 gene mutations), and Alzheimer'sdiseases (3 PSEN1 gene mutations), as well as CMT2A (3 Mfn2 genemutations). These studies show evidence that mitofusin agonists markedlyenhance or improve mitochondrial function (e.g., trafficking) in ALS andconfer a modest benefit in Huntington's disease (see e.g., FIG. 56,TABLE 11). FCCP treatment shows effects of complete mitochondrialuncoupling.

TABLE 11 Primary patient-derived fibroblasts used for Regeneurin-Cstudies Subject ID Fibrob ID Diseases Gender Age Genes Mutation Source PNDS00108 ND34730 Alzheimer's M — PSEN1 GLU184ASP NIH 4 NDS00114 ND34732Alzheimer's F — PSEN1 MET146ILE NIH 4 NDS00115 ND34733 Alzheimer's M —PSEN1 PRO264LEU NIH 4 NDS00125 ND29415 ALS M 51 SOD1 LEU144PRO NIH 2NDS00129 ND29523 ALS M 47 SOD1 LEU38VAL NIH 2 NDS00211 ND32969 ALS M 59SOD1 ILE113THR NIH 6 NDS00090 ND33392 Huntington's F 29 HD CAG:57 NIH 2NDS00093 ND29970 Huntington's M 65 HD CAG:40 NIH 2 NDS00189 ND40536Huntington's F — HD CAG:66 NIH 2 NDS00009 ND33879 Parkinson's F 66 LRRK2GLY2019SER NIH 2 NDS00012 ND29969 Parkinson's F 61 PARK2 ARG275TRP NIH 2NDS00228 ND40066 Parkinson's M 64 PINK1 ILE368ASN NIH 6 NDS00035 ND34769Control F 68 — — NIH 2 NDS00047 ND36320 Control F 71 — — NIH 2 NDS00126ND29510 Control F 55 — — NIH 2 NDS00085 ND29178 Control M 66 — — NIH 7NDS00036 ND34770 Control M 72 — — NIH 2 NDS00059 ND38530 Control M 55 —— NIH 5 CMT2A MFN2 HIS361TYR Baloh CMT2A MFN2 THR105MET Baloh CMT2A MFN2ARG274TRP Barbara 2

Development of a Preclinical Mouse Model of CMT2A

Multiple mouse knock-ins of human CMT2A Mfn2 mutations have notdeveloped typical CMT2A neuropathology. High-level transgenic expressionof human CMT2A Mfn2 mutants can cause pathology, but the phenotypes arenot limited to the neurological system as in human disease. Because asuitable animal model of CMT2A did not exist a mouse was developedhaving conditional, motor-neuron-specific expression of human Mfn2 T105M(one of the CMT2A mutants used in the presently described in vitro andex vivo studies (see e.g., Example 5)). Initial studies of these miceindicate that they develop progressive sciatic nerve CMAP (compoundmotor action potential) abnormalities (decreased CMAP amplitude)accompanied by impaired neuromuscular function (Rotarod latency) (seee.g., FIG. 57). These features are characteristic of the humancondition. Moreover, the efficacy of Regeneurin-S was alreadydemonstrated to rapidly correct mitochondrial dysmotility in sciaticnerves of these mice (see e.g., Example 5). It was planned to use thismodel for in vivo assessment of mitofusin agonist efficacy for CMT2A.Standard mouse models for ALS suitable for in vivo efficacy studies areavailable from Jackson Labs (JAX). A target product profile is shown inTABLE 12, below.

TABLE 12 Preliminary target product profile for mitofusin agonists totreat CMT2A. Product targets Minimal acceptable result Ideal resultPrimary indication Chronic therapy that retards Chronic therapy thatreverses progression of axonal axonal neuropathy in CMT2A neuropathy inCMT2A Patient population Children with a new genetic Patients of allages with mild to diagnosis of CMT2A and moderate genetically patientsof all ages with diagnosed CMT2A genetically diagnosed mild to CMTNeuropathy Score ≤20 moderate CMT2A Treatment duration Chronic ChronicDelivery mode IM injection Transdermal Dosage form Prefilled vialsTransdermal patch Regimen Once a week Once a week Efficacy Delay inperipheral neuropathy Reversal or absence of progression over 3 yearsprogression of peripheral compared to placebo, neuropathy compared toassessed by slower increase in placebo, as indicated by lower modifiedcomposite CMT or stable modified composite Neuropathy Score* CMTNeuropathy Score* Risk/side effect Devoid of local injection effectDevoid of local patch effect and and clinically meaningful CNS, anysystemic side effects cardiac or muscular side effects Therapeuticmodality Small molecule peptidonninnetic Small molecule peptidonninnetic*Mannil M et al Neuromuscul Disord 24:1003-17, 2014

Example 8: In Vivo Administration of Regeneurin-C/O Reverses theCharacteristic Mitochondrial Immobility in Sciatic Nerve Axons

The following example describes in vivo administration of Regeneurin-C/Oto CMT2A mice (IM, 2 mg/kg) reverses the characteristic mitochondrialimmobility in sciatic nerve axons (assessed 4 hours later).

10 week old CMT2A MFN2 T105M mice were injected IM with Mfn agonistRegeneurin-C/O 2 mg/kg twice, or vehicle. Sciatic nerve mitochondrialmotility was measured 4 hours later. Results described in FIG. 58 arefor 2 CMT2A mice per group. As demonstrated herein, these mitofusinagonists can correct mitochondrial motility.

What is claimed is:
 1. A compound of formula (I):

wherein, R¹ is selected from the group consisting of

R² is selected from the group consisting of

R³ is selected from the group consisting of hydrogen (H) and C₁₋₈ alkyl;R⁴ is selected form the group consisting of hydrogen (H) and C₁₋₈ alkyl;A is SO or SO₂; X is N; Y is N; and Z is a linker group selected fromthe group consisting of a bond and C₁₋₆ alkyl; wherein, R¹ or R² areoptionally substituted by one or more of: acetamide, C₁₋₈alkoxy, amino,azo, Br, C₁₋₈alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo, indole, nitrile,phenyl, or thiophene; and optionally further substituted with one ormore acetamide, alkoxy, amino, azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl,Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl,hydroxyl, F, halo, indole, nitrile, phenyl, or thiophene; wherein, thealkyl, cycloalkyl, heteroaryl, heterocyclyl, indole, or phenyl, isoptionally further substituted with one or more selected from the groupconsisting of acetamide, alkoxy, amino, azo, Br, C₁₋₈alkyl, carbonyl,carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, hydroxyl, F, halo, indole, nitrile, phenyl, and thiophene.2. The compound of claim 1, wherein, R³ or R⁴ are substituted by one ormore of: acetamide, C₁₋₈alkoxy, amino, azo, Br, C₁₋₈alkyl, carbonyl,carboxyl, Cl, cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈heterocyclyl, hydroxyl, F, halo, indole, nitrile, phenyl, or thiophene;and optionally further substituted with one or more acetamide, alkoxy,amino, azo, Br, C₁₋₈ alkyl, carbonyl, carboxyl, Cl, cyano, C₃₋₈cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F, halo,indole, nitrile, phenyl, or thiophene; wherein, the alkyl, cycloalkyl,heteroaryl, heterocyclyl, indole, or phenyl, is optionally furthersubstituted with one or more selected from the group consisting ofacetamide, alkoxy, amino, azo, Br, C₁₋₈alkyl, carbonyl, carboxyl, Cl,cyano, C₃₋₈ cycloalkyl, C₃₋₈ heteroaryl, C₃₋₈ heterocyclyl, hydroxyl, F,halo, indole, nitrile, phenyl and thiophene.
 3. The compound of claim 1,selected from the group consisting of:


4. A pharmaceutical composition comprising the compound of claim 1.